X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5.6
Temperature 277.15
Details 0.17 M Ammonium acetate; 0.085 M Sodium citrate pH 5.6; 25.5%(w/v) PEG 4000; 15%(v/v) Glycerol

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 72.22 α = 90
b = 104.07 β = 90
c = 114.45 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 DECTRIS PILATUS 6M -- 2015-03-19
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SLS BEAMLINE X10SA 0.99983 SLS X10SA

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
2.38 44.85 99.7 0.066 -- -- 6.4 -- 35499 -- -3.0 58.906
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)
2.38 2.5 99.9 0.598 -- 3.11 -- --

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 2.38 44.85 -- 0.0 -- 33123 1746 100.0 -- 0.2271 0.2243 0.2772 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 2.381 2.443 -- 112 2126 0.337 0.45 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 55.997
Anisotropic B[1][1] -0.44
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 3.6
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -3.17
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_2_deg 40.41
r_dihedral_angle_1_deg 15.346
r_mcangle_it 2.14
r_chiral_restr 0.133
r_angle_other_deg 1.034
r_bond_other_d 0.016
r_angle_refined_deg 1.9
r_dihedral_angle_4_deg 15.705
r_dihedral_angle_3_deg 21.123
r_gen_planes_refined 0.008
r_scbond_it 3.189
r_mcbond_it 1.111
r_scangle_it 5.159
r_bond_refined_d 0.021
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3655
Nucleic Acid Atoms 0
Heterogen Atoms 30
Solvent Atoms 119

Software

Software
Software Name Purpose
XSCALE data scaling
PHASER phasing version: 2.3.0
REFMAC refinement version: 5.6.0117
PDB_EXTRACT data extraction version: 3.20
XSCALE data reduction
PHASER phasing