目录

  • 1 第一单元
    • 1.1 版权声明
    • 1.2 晶体衍射实验实践指导
    • 1.3 晶体学介绍
    • 1.4 衍射实验室培训方案
    • 1.5 晶体衍射实验的总体步骤
    • 1.6 晶体图片
  • 2 晶体上样操作
    • 2.1 仪器开关机步骤
    • 2.2 液氮cryo开关操作
    • 2.3 晶体样品装样过程
    • 2.4 显微镜下的晶体挑选
    • 2.5 衍射实验-晶体上样及对心介绍
    • 2.6 晶体对心过程
    • 2.7 Synergy仪器的开关门及上样
    • 2.8 FRX仪器的开关门及上样
    • 2.9 大分子晶体预先冷冻上样方法
    • 2.10 测角头事故案例
    • 2.11 封管测试方法
  • 3 数据收集软件操作
    • 3.1 晶体衍射实验软件操作
    • 3.2 CrysAlispro-小分子数据采集
      • 3.2.1 测试时长
    • 3.3 CrysAlispro-大分子晶体粗筛设置
    • 3.4 高温实验操作步骤
    • 3.5 晶体衍射数据质量判定
    • 3.6 twin indexing
    • 3.7 append data collection
  • 4 结构解析和精修
    • 4.1 结构解析介绍
    • 4.2 分析软件安装
      • 4.2.1 software updates - platon
      • 4.2.2 software updates - shelx
    • 4.3 结构解析操作
    • 4.4 checkcif report -olex2
    • 4.5 checkcif report - server
    • 4.6 CIF文件生成晶体学数据表
    • 4.7 晶体数据处理并生成MTZ
    • 4.8 晶面指标化-drag mode
    • 4.9 晶面指标化-snap mode
    • 4.10 去除精修的限制命令
    • 4.11 如何查看分析结果-cif文档?
    • 4.12 对称轴上的无序精修-part -1
    • 4.13 EXYZ和EADP-OLEX2
    • 4.14 phasing simulated annealing and refinement
    • 4.15 position disorder modeling - two methods
    • 4.16 phasing - shelxD
    • 4.17 EXYZ-disorder modeling
    • 4.18 Fragment DB application case
    • 4.19 import model using OLEX2
    • 4.20 add symmetry via Platon
    • 4.21 part-1 Na3HCO3CO3
    • 4.22 phasing by MR(分子置换)with PHENIX
    • 4.23 checkcif using platon
  • 5 粉末衍射技术
    • 5.1 粉末衍射样品制备
    • 5.2 简易的粉末衍射零点校正方法
    • 5.3 粉末衍射实验 - 步长0.02?
    • 5.4 结晶度
    • 5.5 实操-寻峰与报告
    • 5.6 溶剂体积计算软件
    • 5.7 择优取向对峰强和峰位置的影响
    • 5.8 样品研磨过筛与不研磨样品测试差异
  • 6 蛋白结构精修
    • 6.1 tutorial结构精修
  • 7 晶体结构缺陷分析技术
    • 7.1 案例1-弥散散射-对分布函数
    • 7.2 案例2-diffuse scattering
    • 7.3 run discus
    • 7.4 read and plot
      • 7.4.1 build a crystal
      • 7.4.2 build a disordered crystal
      • 7.4.3 disorder and vacancy
    • 7.5 RMC fitting to pdf date
  • 8 checkcif回复及其修正
    • 8.1 VRF回复方法
    • 8.2 412_ALERT_2_B and 417_Alert_2_A and 416
    • 8.3 PLAT342_ALERT_3_B回复
    • 8.4 THETM01_ALERT_3_A
    • 8.5 PLAT029_ALERT_3_A
    • 8.6 PLAT910_ALERT_3_B
    • 8.7 PLAT035_ALERT_1_B
    • 8.8 Short H--H contacts
    • 8.9 196_alert_1_B no temp
    • 8.10 312_alert_2_A
    • 8.11 415_alert_2_A
    • 8.12 430_alert_2_A
    • 8.13 O70_Alert_1_A
    • 8.14 934_ALERT_3_A
    • 8.15 316_ALERT_2_A
    • 8.16 413_414_ALERT_2_A
    • 8.17 O35_ALERT_1_B
    • 8.18 196_ALERT_1_B
    • 8.19 112_ALERT_2_B
    • 8.20 417/410_short d-h and h-h
  • 9 审稿人意见回复案例
    • 9.1 实际案例1-限制与对称
    • 9.2 实际案例2- atom list out of sequence
  • 10 虚拟仿真实验
    • 10.1 虚拟仿真实验体验介绍
    • 10.2 虚拟仿真实验体验项目
  • 11 FAQ常见问题
    • 11.1 如何查看晶体结构?
    • 11.2 TwinRot不正常工作
    • 11.3 twin检测
    • 11.4 OLEX多个溶剂分子的输入格式
    • 11.5 如何生成二维衍射图片
    • 11.6 如何判断预实验结果的好坏?
    • 11.7 什么样的数据才能用于结构解析?
    • 11.8 如何查看晶体在测试过程中是否移动?
    • 11.9 衍射点拖尾能用来解析结构吗?
    • 11.10 label atom and bond
    • 11.11 Z and Z'
    • 11.12 Laue group 和 点群
    • 11.13 flack参数的意义
    • 11.14 0.63的占位可以限制在0.5吗?
    • 11.15 P21 或者 P21C
    • 11.16 rms sigma / rms deviation
    • 11.17 how to use CCDC
    • 11.18 change asymmetric unit
    • 11.19 change asymmetric unit - H2O
    • 11.20 data collection and refinement for paper writing
    • 11.21 变换晶胞参数取向和空间群
    • 11.22 查看无序分子占位信息
    • 11.23 crystalline boundary 晶界
    • 11.24 移除无序部分,保存为有序结构-1
    • 11.25 移除无序部分,保存为有序结构-2
    • 11.26 C2/c or I2/a? which one should be choosed?
    • 11.27 Conventional and reduced cell
    • 11.28 twinning introduction
    • 11.29 same.sadi mismatch
    • 11.30 TITL error
    • 11.31 COD结构数据库应用-查找AlF3
    • 11.32 Rint for HKLF4 and HKLF5
    • 11.33 optimal crystal size and shape
    • 11.34 修改datablock的名称
    • 11.35 cif生成粉末衍射图和比对
  • 12 结晶实验操作
    • 12.1 结晶实验-结晶机器人操作
      • 12.1.1 结晶机器人操作
      • 12.1.2 结晶机器人关机步骤
      • 12.1.3 LCP设置不当与96板运行
      • 12.1.4 仪器未按照流程关机事故
      • 12.1.5 毛刷清洗
      • 12.1.6 非正常暂停后重启仪器步骤
      • 12.1.7 泵的开关on 还是off
    • 12.2 使用常见误操作
      • 12.2.1 96针清洗没有清洗
      • 12.2.2 水槽没有归位
      • 12.2.3 导向板未归位
    • 12.3 维护
      • 12.3.1 查看96针状态
      • 12.3.2 导板不能下滑
    • 12.4 考核方法
  • 13 JAN UVEX-P 操作
    • 13.1 UVEX - P 操作步骤
    • 13.2 问题1 - 紫外过曝使用
  • 14 液体配比仪操作
实际案例1-限制与对称

Comments of Reviewer # 2 and response by the authors

 We would like to thank referees for taking the time to reviewour manuscript and thank the referee 2 for pointing out the potential problemsof three crystal structures. We have addressed your comments below and feelthat the work is greatly improved as a result of your input. In what followsthe referees’ comments are in black and the authors’ responses are in blue.

The structure of racemic 6 is more interesting. It seems torefine satisfactorily, with a conventional R of 6%, but the refinement wasconducted with nearly 5000 restraints! What is going on here?

 We understand the concern of the reviewer. The 5000 restraintsare primarily as a result of the applied default DELU and SIMU with no atoms specified(all non-hydrogen atoms are assumed) to facilitate the stable refinement of theanisotropic displacement parameters of the side chains. When the DELU and SIMUwere removed, displacement ellipsoids of some atoms on the side chains became somewhatelongated because of the dynamic disorders of these side chains. The list of“summary of restraints applied” was checked and did not show strong deviations,indicating these restraints were appropriately applied.

 There might be better restraint strategy which we do not foreseeto modeling atomic displacement parameters of the highly disordered side chains.

 When I examined the packing, it seemed to me that the entiremolecule was disordered across a mirror plane, but of course there is no mirrorplane in the chiral space group C2. I took the hkl file supplied in the CIF andran it through XPREP. There, the space group with the best figure of merit (byfar) is C2/m, which naturally contains the missing mirror plane. Structureslike this, where a molecule resides on a site with crystallographic symmetrythat the molecule itself cannot possess, are not at all uncommon. The trick isto carry out the refinement using a PART -1 command for the entire molecule,which is given half occupancy. The other half molecule is then generated bysymmetry. Such a refinement should eliminate the majority of the thousands ofrestraints used in the present work, even if the R is not lowered significantly.

After some consideration, the authors mayconclude that C2 is the correct space group for racemic 6 (it's notimpossible), but they need to justify this choice. Furthermore, the discussionof the crystal structures should at least mention the gross disorder present.

 Thank you for this suggestion. We agree that the space group C2/mfor this crystal structure is not impossible. However, our attempts tore-refine the structure using a PART -1 command in C2/m was unsatisfactory (R1= 12.61%). It is primarily the tert-butyl group that appears randomly orientedand unable to accommodate C2/m. Space group C2 describes the structure betterthan C2/m and the mirror symmetry is the pseudo-symmetry operator. The twomolecules are not quite related by a crystallographic mirror symmetry elements ofa higher-symmetric space group C2/m.