X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5.5
Temperature 298.0
Details 40 mM sodium cacodylate, 20 mM hexamine Co(III) chloride, 20 mM MgCl2

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 31.17 α = 90
b = 31.17 β = 90
c = 84.32 γ = 90
Symmetry
Space Group P 43 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MAR scanner 300 mm plate -- 2015-07-24
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 21-ID-D 0.91833 APS 21-ID-D

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
1.2 50 99.7 0.145 -- -- 14.1 -- 13758 -- -- --
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)
1.2 1.22 100.0 0.584 -- -- 8.1 --

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 1.2 29.24 -- 0.0 -- 12988 708 99.6 -- 0.121 0.12 0.157 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 1.2 1.23 -- 46 900 0.14 0.161 -- 98.44
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 12.42
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] -0.01
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_other 0.296
r_angle_refined_deg 42.196
r_bond_other_d 2.887
r_gen_planes_refined 0.223
r_bond_refined_d 1.823
r_chiral_restr 3.623
r_rigid_bond_restr 14.638
r_sphericity_free 57.545
r_scbond_it 1.468
r_sphericity_bonded 7.632
r_angle_other_deg 56.801
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 0
Nucleic Acid Atoms 338
Heterogen Atoms 28
Solvent Atoms 126

Software

Software
Software Name Purpose
REFMAC refinement version: 5.8.0073
HKL-2000 data collection
HKL-2000 data scaling
SHELX phasing
PDB_EXTRACT data extraction version: 3.15
HKL-2000 data reduction