X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 292.0
Details 0.2 M magnesium formate dehydrate pH 7.0 and 20 % w/v PEG 3350

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 36.64 α = 90
b = 62.52 β = 99.13
c = 43.19 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 PILATUS 6M-F -- 2017-04-23
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04

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
1.4 36.18 99.5 0.072 -- -- 3.9 147995 37737 -- -- --
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)
1.4 1.42 95.6 0.796 -- 1.3 2.7 --

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
SAD 1.4 35.25 -- 0.0 -- 35875 1841 99.44 -- 0.1537 0.1525 0.1751 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 1.4 1.436 -- 142 2552 0.29 0.275 -- 96.52
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 12.773
Anisotropic B[1][1] -1.06
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.27
Anisotropic B[2][2] 0.12
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.97
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_2_deg 33.897
r_gen_planes_other 0.014
r_bond_refined_d 0.009
r_dihedral_angle_1_deg 7.349
r_gen_planes_refined 0.01
r_dihedral_angle_4_deg 7.853
r_mcbond_it 0.841
r_angle_other_deg 2.443
r_dihedral_angle_3_deg 12.105
r_angle_refined_deg 1.565
r_chiral_restr 0.081
r_mcbond_other 0.829
r_mcangle_it 1.292
r_bond_other_d 0.037
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1657
Nucleic Acid Atoms 0
Heterogen Atoms 3
Solvent Atoms 217

Software

Software
Software Name Purpose
REFMAC refinement version: 5.8.0238
PDB_EXTRACT data extraction version: 3.22
xia2 data reduction
Aimless data scaling
CRANK2 phasing