目录

  • 1 第一单元
    • 1.1 晶体衍射实验实践指导
    • 1.2 晶体学介绍
  • 2 晶体上样操作
    • 2.1 衍射实验-晶体上样及对心介绍
    • 2.2 晶体样品装样过程
    • 2.3 显微镜下的晶体挑选
    • 2.4 Synergy仪器的开关门及上样
    • 2.5 FRX仪器的开关门及上样
    • 2.6 大分子晶体预先冷冻上样方法
    • 2.7 晶体对心过程
  • 3 数据收集软件操作
    • 3.1 CrysAlispro-小分子数据采集
    • 3.2 CrysAlispro-大分子晶体粗筛设置
    • 3.3 晶体衍射实验仪器操作
    • 3.4 晶体衍射数据质量判定
  • 4 结构解析和精修
    • 4.1 结构解析介绍
    • 4.2 分析软件安装
    • 4.3 结构解析操作
    • 4.4 checkcif report生成
    • 4.5 CIF文件生成晶体学数据表
    • 4.6 蛋白晶体数据处理
    • 4.7 晶面指标化
    • 4.8 移除无序部分,保存为有序结构
    • 4.9 去除精修的限制命令
  • 5 checkcif回复及其修正
    • 5.1 412_ALERT_2_B修正
    • 5.2 PLAT342_ALERT_3_B回复
    • 5.3 THETM01_ALERT_3_A
    • 5.4 PLAT029_ALERT_3_A
    • 5.5 PLAT910_ALERT_3_B
    • 5.6 VRF回复方法
  • 6 审稿人意见回复案例
    • 6.1 实际案例1-限制与对称
  • 7 虚拟仿真实验
    • 7.1 虚拟仿真实验体验介绍
    • 7.2 虚拟仿真实验体验项目
  • 8 FAQ常见问题
    • 8.1 如何查看晶体结构?
    • 8.2 TwinRot不正常工作
    • 8.3 twin检测
    • 8.4 OLEX多个溶剂分子的输入格式
    • 8.5 如何生成二维衍射图片
    • 8.6 如何判断预实验结果的好坏?
  • 9 结晶实验操作
    • 9.1 结晶实验-结晶机器人操作
      • 9.1.1 结晶机器人操作
      • 9.1.2 结晶机器人关机步骤
      • 9.1.3 LCP设置不当与96板运行
      • 9.1.4 仪器未按照流程关机事故
  • 10 JAN UVEX-P 操作
    • 10.1 UVEX - P 操作步骤
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.