X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 279.15
Details PEG 8000, Tris-HCl

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 41.72 α = 90
b = 52.68 β = 90
c = 89.18 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-F -- 2015-05-18
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON DIAMOND BEAMLINE I02 0.97949 Diamond I02

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
1.3 45.36 98.1 0.07 -- -- 5.0 -- 48076 -- -- --
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)
1.3 1.32 84.1 0.62 -- 1.7 3.2 2103

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 1.3 45.36 -- -- -- 45723 2297 97.71 -- 0.1336 0.13213 0.16324 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 1.3 1.334 -- 156 2834 0.28 0.283 -- 83.94
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 19.083
Anisotropic B[1][1] 0.05
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.04
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.01
RMS Deviations
Key Refinement Restraint Deviation
r_chiral_restr 0.163
r_rigid_bond_restr 6.035
r_mcbond_it 2.898
r_scbond_it 4.338
r_sphericity_bonded 10.596
r_bond_other_d 0.002
r_angle_refined_deg 2.343
r_dihedral_angle_1_deg 6.064
r_dihedral_angle_3_deg 10.535
r_scbond_other 4.339
r_dihedral_angle_4_deg 19.993
r_gen_planes_refined 0.013
r_mcbond_other 2.898
r_gen_planes_other 0.002
r_mcangle_it 3.205
r_scangle_other 5.587
r_bond_refined_d 0.028
r_long_range_B_other 5.563
r_angle_other_deg 1.196
r_long_range_B_refined 5.564
r_sphericity_free 23.194
r_mcangle_other 3.203
r_dihedral_angle_2_deg 32.974
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1266
Nucleic Acid Atoms 0
Heterogen Atoms 29
Solvent Atoms 182

Software

Software
Software Name Purpose
REFMAC refinement version: 5.8.0103
SCALA data scaling
PDB_EXTRACT data extraction version: 3.20
MOSFLM data reduction
PHASER phasing