X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.5
Temperature 291.0
Details 0.1 M Bis-Tris, 0.2 M Magnesium Chloride, 10 % PEG3350

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 113.39 α = 90
b = 202.65 β = 90
c = 315.14 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 CRL Transfocator 2015-08-20
Diffraction Radiation
Monochromator Protocol
Si (111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 0.9763 PETRA III, EMBL c/o DESY P14 (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
1.9 170.45 97.5 0.087 -- -- 5.04 -- 526170 -- -- --
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)
1.9 2.0 99.4 -- -- 0.83 -- --

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
FOURIER SYNTHESIS 1.9 170.45 -- -- -- 526170 27607 97.82 -- 0.18967 0.18783 0.22508 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 1.9 1.949 -- 1810 34608 0.392 0.391 -- 87.3
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 49.054
Anisotropic B[1][1] -1.68
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.87
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.81
RMS Deviations
Key Refinement Restraint Deviation
r_angle_other_deg 1.41
r_bond_refined_d 0.019
r_dihedral_angle_4_deg 18.26
r_mcangle_other 1.878
r_mcbond_it 1.169
r_mcbond_other 1.169
r_dihedral_angle_2_deg 35.203
r_scbond_it 1.903
r_chiral_restr 0.128
r_gen_planes_refined 0.01
r_gen_planes_other 0.006
r_dihedral_angle_3_deg 15.716
r_scbond_other 1.903
r_scangle_other 2.718
r_dihedral_angle_1_deg 7.411
r_long_range_B_other 8.391
r_mcangle_it 1.878
r_long_range_B_refined 8.391
r_angle_refined_deg 1.971
r_bond_other_d 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 47836
Nucleic Acid Atoms 0
Heterogen Atoms 292
Solvent Atoms 3542

Software

Software
Software Name Purpose
REFMAC refinement version: 5.8.0103
PDB_EXTRACT data extraction version: 3.20
XDS data reduction
XSCALE data scaling