X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.5
Temperature 291.0
Details 0.1M MES, 30%(w/v) PEG 1500, 0.01M Betaine hydrochloride, pH 5.5, vapor diffusion, hanging drop, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 80.47 α = 90
b = 80.47 β = 90
c = 290.9 γ = 120
Symmetry
Space Group P 32

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RAYONIX MX-300 -- 2010-10-22
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 21-ID-D 0.9795 APS 21-ID-D

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
3 30 98.4 0.066 -- -- 3.2 -- 41487 -- -- --
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)
3.0 3.11 96.7 0.621 -- -- 3.1 4103

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 3.0 29.89 -- 0.0 -- 41434 2088 98.3 -- 0.2089 0.2059 0.2677 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 3.001 3.078 -- 175 2816 0.355 0.397 -- 95.87
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 107.409
Anisotropic B[1][1] 0.29
Anisotropic B[1][2] 0.14
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.29
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.43
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_refined 0.006
r_chiral_restr 0.094
r_dihedral_angle_4_deg 18.601
r_dihedral_angle_3_deg 18.679
r_dihedral_angle_2_deg 35.638
r_dihedral_angle_1_deg 6.973
r_angle_refined_deg 1.433
r_bond_refined_d 0.01
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 11926
Nucleic Acid Atoms 0
Heterogen Atoms 66
Solvent Atoms 0

Software

Computing
Computing Package Purpose
SCALEPACK Data Reduction (data scaling)
PHASER Structure Solution
REFMAC 5.6.0117 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
REFMAC5 version: 5.6.0117 refinement
Phaser molecular replacement
SCALEPACK data reduction