X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 293.0
Details 25%(w/v) PEG 2000 MME, 10%(v/v) Glycerol, 0.1M Na-HEPES (pH 7.0), vapor diffusion, hanging drop, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 85.99 α = 90
b = 66.98 β = 90
c = 68.53 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS VII Osmic VariMax mirrors 2007-10-27
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418 -- --

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot
1.47 30.09 89.3 -- 0.061 -- 5.8 60224 60224 -- -- --
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
1.47 1.51 22.5 0.28 0.28 2.8 1.6 1092

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
MOLECULAR REPLACEMENT 1.47 21.52 -- 0.0 -- 60170 3040 88.52 -- 0.1655 0.164 0.1928 RANDOM
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 1.47 1.51 -- 47 841 0.2441 0.2266 -- 88.52
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 20.3331
Anisotropic B[1][1] -3.0805
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.8644
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.2161
RMS Deviations
Key Refinement Restraint Deviation
t_other_torsion 16.64
t_omega_torsion 3.95
t_angle_deg 1.05
t_bond_d 0.01
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.155
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2775
Nucleic Acid Atoms 0
Heterogen Atoms 73
Solvent Atoms 542

Software

Computing
Computing Package Purpose
CrystalClear Data Collection
XDS Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
PHASER Structure Solution
BUSTER 2.11.2 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
BUSTER-TNT version: BUSTER 2.11.2 refinement
Phaser version: 2.1.4 molecular replacement
SCALA version: 3.3.15 data reduction