X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5.5
Temperature 277.0
Details 18% PEG3350, 0.1 M sodium citrate tribasic, pH 5.5

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 41.68 α = 90
b = 111.33 β = 90
c = 139.39 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 PILATUS3 6M K-B pair of biomorph mirrors for vertical and horizontal focusing 2017-08-09
Diffraction Radiation
Monochromator Protocol
double crystal Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 23-ID-D 1.033100 APS 23-ID-D

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
2.1 86.99 99.2 0.048 -- -- 3.5 -- 38500 -- -- 38.0
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)
2.1 2.16 97.9 0.636 -- 1.6 3.4 --

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 2.1 86.99 -- -- -- 36554 1900 98.72 -- 0.20222 0.2004 0.23608 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 2.098 2.153 -- 138 2603 0.3 0.299 -- 97.3
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 54.091
Anisotropic B[1][1] -0.2
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.78
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.58
RMS Deviations
Key Refinement Restraint Deviation
r_long_range_B_refined 7.286
r_dihedral_angle_3_deg 13.61
r_angle_refined_deg 1.312
r_mcangle_other 4.269
r_mcbond_other 2.86
r_dihedral_angle_1_deg 5.833
r_scangle_other 5.248
r_gen_planes_refined 0.005
r_bond_other_d 0.001
r_mcangle_it 4.27
r_bond_refined_d 0.01
r_scbond_it 3.345
r_scbond_other 3.345
r_mcbond_it 2.863
r_dihedral_angle_2_deg 33.763
r_gen_planes_other 0.001
r_dihedral_angle_4_deg 17.874
r_angle_other_deg 0.901
r_chiral_restr 0.074
r_long_range_B_other 7.184
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3767
Nucleic Acid Atoms 0
Heterogen Atoms 17
Solvent Atoms 236

Software

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