Crystallography

Crystallographic Theory

• Basics of Crystallography
• Phase problem, and Phasing
• Twinning
• R-factors
• Bulk solvent correction
• Fiber diffraction
• Disorder
• References and links

Procedures

• Solving a structure
• Solve a small-molecule structure
• Model building and refinement
• Model Evaluation and Interpretation

Crystallography Software

For Specific Tasks

• Data reduction
• Molecular replacement (MR)
• Substructure determination
• Experimental phasing (SIR/MIR and SAD/MAD)
• Electron density modification
• Automated Model building
• Interactive Model building
• Refinement
• Model validation
• Model Evaluation
• Loop modelling

Automated Pipelines for Structure Solution

• Ants
• Auto-Rickshaw (Structure determination)
• autoSHARP
• BALBES
• BNP
• CRANK
• Elves
• MrBUMP - molecular replacement
• Phenix - comprehensive package
• HKL2MAP - SAD/MAD/SIRAS/SIR phasing based on SHELXC/D/E

Web services

• ARP/wARP web services (model building)
• Auto-Rickshaw (Structure determination) - see example at xds:1RQW
• Bias removal server
• York suite (Balbes, Modsearch, Zanuda)
• Diffraction Anisotropy Server
• Bravais Lattice Determination by Projections
• brute force MR - with up to the full set of SCOP domains (100k) to attempt a Phaser MR placement of each domain. The server then ranks the results, allowing you to identify a single well placed domain. PNAS paper at [1].
• Fitmunk takes a PDB and MTZ file, and helps to identify your protein by electron density based sequencing, and by fitting different conformations. See https://www.ncbi.nlm.nih.gov/pubmed/26894674 and https://www.ncbi.nlm.nih.gov/pubmed/26660914
• STARANISO analyses, corrects and visualises diffraction data for data anisotropy; see also PDBpeep for deposited PDB entries.
• Grade to create restraint dictionaries for refinement

Software Packages

(large packages first)

• CCP4
• CNS
• PHENIX
• SHELX C/D/E and SHELXL (homepage at [2], overview paper)
• moleman, lsqman, ... from Uppsala Software Factory
• XDS homepage and XDSwiki
• HKL homepage
• COOT
• PyMol wiki
• CCP4mg
• O
• ARP/wARP
• SHARP homepage
• Solve/Resolve
• PDB coordinates to Restraints - This Web-server generates custom RNA/DNA base stacking and base pairing restraints for crystallographic refinement. Input is in PDB format. Output is Pymol , CNS and PHENIX formatted.
• Global Phasing Ltd (data processing, structure solution, refinement - BUSTER, SHARP/autoSHARP, autoPROC, Grade, Rhofit, Pipedream, STARANISO)

Libraries for crystallography and related areas

• Clipper
• Crystallographic Toolbox
• CCP4 library; documentation at [3]
• mmdb

Tips and Tricks

• Finding symmetry elements in P1
• Programs to convert X-ray diffraction image file formats to graphics file formats

Teaching crystallography

The effect of resolution on electron density

• James Holton's movie [[4]]

Understanding and extending the properties and limitations of crystallographic computations

Ensemble refinement, and molecular dynamics

1. Direct Observation of Protein Solvation and Discrete Disorder with Experimental Crystallographic Phases. Burling FT, Weis WI, Flaherty KM, Brünger AT. Science (1996) 271, 72-77 [5]
2. Heterogeneity and Inaccuracy in Protein Structures Solved by X-Ray Crystallography. DePristo MA,de Bakker PIW, Blundell TL (2004) Structure 12, 831-838 [6]
3. Ensemble Refinement of Protein Crystal Structures: Validation and Application. Levin EJ, Kondrashov DA, Wesenberg GE, Phillips GN, Structure 15, 1040 - 1052 [7]
4. A comparison between molecular dynamics and X-ray results for dissociated CO in myoglobin. Vitkup D, Petsko GA, Karplus M. Nature Structural Biology 4, 202 - 208 (1997) [8] (Vitkup et al showed that fitting a single model to MD-simulation derived "data" gave ~20% R, which means multiple conformers are sufficient to explain the "R-Factor Gap" between the 20% usually obtained for macromolecules, and the 5% routinely obtained for small molecules)

Electron microscopy and X-ray

1. Elucidating the medium-resolution structure of ribosomal particles: an interplay between electron cryo-microscopy and X-ray crystallography. Harms J, Tocilj A, Levin I, Agmon I, Stark H, Kölln I, van Heel M, Cuff M, Schlünzen F, Bashan A, Franceschi F, Yonath A. Structure 7, 931-941 (1999) [9]

NMR versus X-ray

A couple of papers analysing and comparing NMR and X-ray methods/structures:

1. Combining experimental information from crystal and solution studies: joint X-ray and NMR refinement. Shaanan B, Gronenborn AM, Cohen GH, Gilliland GL, Veerapandian B, Davies DR, Clore GM. Science (1992), 257, 961 [10]
2. X-ray Crystallography and NMR: Complementary Views of Structure and Dynamics, Nature Structural Biology 4, 862-865 (1997). Preprint available from Axel Brunger's "publications" website.
3. Traditional Biomolecular Structure Determination by NMR Spectroscopy Allows for Major Errors. S.B. Nabuurs, C.A.E.M. Spronk, G.W. Vuister, G. Vriend. PLoS Comput Biol 2(2): e9. [11]