X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Temperature 293.15
Details 0.2M Magnesium chloride, 0.1M Tris pH 8, 10% PEG 8000, 1:1 protein to precipitant ratio.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 97.13 α = 90
b = 97.13 β = 90
c = 115.08 γ = 120
Symmetry
Space Group P 31 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2011-08-08
Diffraction Radiation
Monochromator Protocol
Si(111) double crystal 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
2.4 28.34 97.8 0.054 -- -- 3.04 -- 46442 -4.0 -3.0 52.941
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)
2.4 2.46 84.9 0.599 -- 1.78 -- --

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 2.4 28.34 -- -- -- 22416 1992 97.55 -- 0.15823 0.15453 0.20006 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 2.4 2.462 -- 118 1369 0.219 0.318 -- 83.17
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 61.771
Anisotropic B[1][1] -8.85
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -8.85
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 17.7
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_1_deg 8.214
r_gen_planes_other 0.001
r_mcbond_other 4.603
r_mcangle_other 6.136
r_angle_refined_deg 2.372
r_scbond_other 5.7
r_bond_other_d 0.006
r_scbond_it 5.752
r_bond_refined_d 0.028
r_long_range_B_refined 9.664
r_dihedral_angle_2_deg 34.591
r_dihedral_angle_3_deg 15.619
r_chiral_restr 0.147
r_long_range_B_other 9.66
r_mcangle_it 6.138
r_scangle_other 7.931
r_gen_planes_refined 0.014
r_mcbond_it 4.608
r_angle_other_deg 1.188
r_dihedral_angle_4_deg 18.338
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3052
Nucleic Acid Atoms 0
Heterogen Atoms 82
Solvent Atoms 116

Software

Software
Software Name Purpose
REFMAC refinement version: 5.8.0123
Coot model building version: 0.8.1
PHASER phasing version: 1.8.4
XSCALE data scaling version: 03.11.14
XDS data reduction version: 03.11.14