X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.5
Temperature 291.0
Details 0.2 M magnesium chloride, 5 mM manganese chloride, 0.1 M Tris, pH 8.5, 30% w/v PEG4000

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 73.95 α = 90
b = 73.95 β = 90
c = 128.58 γ = 120
Symmetry
Space Group P 64 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD -- 2014-07-16
Diffraction Radiation
Monochromator Protocol
double crystal Si(220) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 22-BM 1.000 APS 22-BM

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
2.22 50 99.8 0.098 -- 31.943 14.1 -- 10855 -- -- --
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)
2.22 2.3 99.9 0.981 -- -- 14.0 1053

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 2.22 50.0 -- 0.0 -- 10308 522 99.9 -- 0.1938 0.1915 0.2411 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 2.222 2.28 -- 44 724 0.249 0.366 -- 99.61
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 44.192
Anisotropic B[1][1] -0.66
Anisotropic B[1][2] -0.33
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.66
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 2.14
RMS Deviations
Key Refinement Restraint Deviation
r_mcbond_other 1.651
r_gen_planes_refined 0.006
r_gen_planes_other 0.001
r_dihedral_angle_2_deg 36.406
r_bond_refined_d 0.012
r_dihedral_angle_1_deg 5.742
r_bond_other_d 0.002
r_mcbond_it 1.653
r_mcangle_it 2.726
r_chiral_restr 0.09
r_dihedral_angle_3_deg 14.256
r_dihedral_angle_4_deg 16.968
r_angle_other_deg 0.956
r_angle_refined_deg 1.483
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1458
Nucleic Acid Atoms 0
Heterogen Atoms 23
Solvent Atoms 61

Software

Software
Software Name Purpose
REFMAC refinement version: 5.8.0123
SERGUI data collection
HKL-2000 data scaling
PHASER phasing
PDB_EXTRACT data extraction version: 3.15
HKL-2000 data reduction