X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7
Temperature 292.0
Details 100 mM HEPES, 200 mM magnesium sulfate, 2-20% PEG 3350

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 81.46 α = 90
b = 81.46 β = 90
c = 137.38 γ = 90
Symmetry
Space Group P 41 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS 6M-F -- 2014-07-13
Diffraction Radiation
Monochromator Protocol
Si (111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92 Diamond I04-1

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
1.95 57.6 99.9 0.054 -- -- 12.9 -- 34608 -- -- 35.38
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)
1.95 2.0 99.8 0.67 -- 4.2 13.5 --

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 1.95 18.22 -- -- -- 32728 1652 99.74 -- 0.20642 0.2055 0.22552 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 1.95 2.0 -- 110 2368 0.29 0.286 -- 99.92
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 40.296
Anisotropic B[1][1] 0.0
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.0
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.0
RMS Deviations
Key Refinement Restraint Deviation
r_chiral_restr 0.095
r_dihedral_angle_1_deg 3.793
r_mcangle_other 4.063
r_dihedral_angle_3_deg 14.491
r_mcbond_other 2.762
r_angle_refined_deg 1.694
r_scangle_other 9.805
r_angle_other_deg 3.673
r_bond_refined_d 0.013
r_long_range_B_refined 11.084
r_mcangle_it 3.942
r_scbond_it 7.344
r_gen_planes_refined 0.01
r_gen_planes_other 0.023
r_scbond_other 7.341
r_long_range_B_other 11.108
r_dihedral_angle_4_deg 17.429
r_bond_other_d 0.0
r_mcbond_it 3.153
r_dihedral_angle_2_deg 34.767
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2173
Nucleic Acid Atoms 0
Heterogen Atoms 38
Solvent Atoms 120

Software

Software
Software Name Purpose
REFMAC refinement version: 5.8.0131
XDS data reduction
PHASER phasing
XSCALE data scaling