X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5
Temperature 291.0
Details 100 mM Citrate, 20% PEG6000

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 54.08 α = 90
b = 70.67 β = 101.13
c = 77.72 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS EIGER X 16M -- 2017-12-07
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 1.0 Australian Synchrotron MX2

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
1.53 39.8 98.7 0.051 -- 12.5 5.2 -- 85118 -- -- --
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)
1.53 1.56 81.7 0.314 -- 2.3 4.9 --

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 1.53 39.779 -- -- -- 80852 4265 98.66 -- 0.15182 0.15041 0.17876 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 1.532 1.572 -- 266 5273 0.202 0.246 -- 87.59
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 22.246
Anisotropic B[1][1] -0.02
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.01
Anisotropic B[2][2] 0.02
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.0
RMS Deviations
Key Refinement Restraint Deviation
r_sphericity_bonded 3.829
r_bond_other_d 0.002
r_mcbond_it 0.742
r_mcangle_it 0.881
r_angle_refined_deg 1.298
r_scbond_it 0.698
r_dihedral_angle_1_deg 5.272
r_angle_other_deg 0.899
r_sphericity_free 15.762
r_scbond_other 0.698
r_dihedral_angle_2_deg 33.756
r_gen_planes_other 0.003
r_mcangle_other 0.881
r_scangle_other 0.741
r_dihedral_angle_3_deg 11.425
r_long_range_B_other 1.509
r_chiral_restr 0.071
r_gen_planes_refined 0.004
r_rigid_bond_restr 0.791
r_bond_refined_d 0.006
r_dihedral_angle_4_deg 16.875
r_mcbond_other 0.742
r_long_range_B_refined 2.208
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3807
Nucleic Acid Atoms 0
Heterogen Atoms 86
Solvent Atoms 759

Software

Software
Software Name Purpose
REFMAC refinement version: 5.8.0189
ADDREF data reduction
Aimless data scaling
PHASER phasing