X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
Temperature 277.0
Details Protein at 5 mg per ml. 0.6 to 0.8 M KCl, 0.9 to 1.2 M (NH4)2SO4, and 100 mM HEPES (pH 7.0)

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 74.29 α = 90
b = 135.29 β = 90
c = 148.67 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 -- 2014-09-26
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92 Diamond I04-1

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 74.34 99.9 0.181 0.17 -- 7.5 -- 101717 -- -- --
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)
2.0 2.03 99.1 4.328 -- 0.5 7.2 --

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 2.0 74.34 -- 0.0 -- 101635 4914 99.85 -- 0.2281 0.2267 0.2548 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 2.0 2.052 -- 343 7041 0.367 0.374 -- 99.25
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 52.6654
Anisotropic B[1][1] -1.32
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.58
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.25
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_3_deg 17.062
r_dihedral_angle_4_deg 15.032
r_mcbond_it 3.96
r_dihedral_angle_2_deg 42.001
r_chiral_restr 0.106
r_scbond_it 4.187
r_dihedral_angle_1_deg 6.514
r_bond_refined_d 0.013
r_mcangle_it 6.122
r_angle_refined_deg 1.742
r_gen_planes_refined 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 8947
Nucleic Acid Atoms 0
Heterogen Atoms 58
Solvent Atoms 492

Software

Software
Software Name Purpose
REFMAC refinement version: 5.8.0123
PDB_EXTRACT data extraction version: 3.10
XDS data reduction
Aimless data scaling
PHASER phasing