X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 4.5
Temperature 293.0
Details 18% PEG 3350, 0.12M Sodium Potassium Phosphate, 6.4% Hexanediol,100mM Sodium citrate pH 4.5, vapour diffusion, sitting drop, temperature 293K, VAPOR DIFFUSION, SITTING DROP

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 146.79 α = 90
b = 135.78 β = 108.82
c = 111.01 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS 6M -- 2010-11-18
Diffraction Radiation
Monochromator Protocol
Sl(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID29 0.9919 ESRF ID29

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
2.02 105.07 98.6 -- 0.082 -- 3.2 133404 133404 -- -- --
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)
2.02 2.07 98.3 0.477 0.477 1.5 2.9 9819

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 2.02 105.075 -- 0.0 -- 133404 6719 98.54 -- 0.1878 0.1866 0.2108 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 2.016 2.068 -- 489 9187 0.269 0.292 -- 98.2
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 38.1013
Anisotropic B[1][1] 0.1
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.06
Anisotropic B[2][2] -0.04
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.02
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_other 0.007
r_gen_planes_refined 0.007
r_chiral_restr 0.08
r_dihedral_angle_4_deg 11.637
r_dihedral_angle_3_deg 13.602
r_dihedral_angle_2_deg 34.204
r_dihedral_angle_1_deg 6.212
r_angle_other_deg 1.403
r_angle_refined_deg 1.49
r_bond_other_d 0.007
r_bond_refined_d 0.009
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 13128
Nucleic Acid Atoms 0
Heterogen Atoms 122
Solvent Atoms 721

Software

Computing
Computing Package Purpose
MxCube Data Collection
XSCALE Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
PHASER Structure Solution
REFMAC 5.6.0119 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
REFMAC5 version: 5.6.0119 refinement
Phaser molecular replacement
SCALA version: 3.3.16 data reduction