X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 7.5
Temperature 293.0
Details 0.1M HEPES pH 7.5; 25% PEG 3350, VAPOR DIFFUSION, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 97.25 α = 90
b = 132.82 β = 90
c = 233.69 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL PSI PILATUS 6M -- 2010-03-06
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON DIAMOND BEAMLINE I24 0.9778 DIAMOND I24

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 97.8 0.153 -- -- 3.0 60032 60032 -3.0 -3.0 --
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 3.16 98.8 0.668 -- 1.6 3.0 8778

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 19.99 -- -- 60032 56650 3019 97.57 0.23133 0.23133 0.22857 0.28264 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 3.0 3.076 -- 234 4094 0.32 0.387 -- 98.59
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 34.252
Anisotropic B[1][1] 3.32
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.74
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.58
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 7.851
r_scbond_it 5.549
r_mcangle_it 3.888
r_mcbond_other 0.314
r_mcbond_it 2.109
r_gen_planes_other 0.001
r_gen_planes_refined 0.004
r_chiral_restr 0.073
r_dihedral_angle_4_deg 17.299
r_dihedral_angle_3_deg 15.324
r_dihedral_angle_2_deg 37.351
r_dihedral_angle_1_deg 5.941
r_angle_other_deg 0.834
r_angle_refined_deg 1.087
r_bond_other_d 0.002
r_bond_refined_d 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 17494
Nucleic Acid Atoms 0
Heterogen Atoms 109
Solvent Atoms 39

Software

Computing
Computing Package Purpose
GDA Data Collection
XDS Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
PHASER Structure Solution
REFMAC 5.5.0110 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.5.0110 refinement
PHASER model building
GDA data collection