X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.5
Temperature 293.0
Details 0.01M cobalt chloride, 1.80M ammonium sulfate, 0.1M MES pH 6.5, Additive - 0.001 M 3-oxo-delta 4,6, Lithocholyl Coenzyme A, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 52.96 α = 90
b = 52.96 β = 90
c = 428.63 γ = 120
Symmetry
Space Group H 3 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 KOHZU: Double Crystal Si(111) 2012-09-19
Diffraction Radiation
Monochromator Protocol
Double Crystal Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 8.2.2 -- ALS 8.2.2

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
2.2 28.58 98.5 0.086 -- -- -- -- 12340 -- -3.0 39.357
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)
2.2 2.28 94.1 0.479 -- 2.9 4.8 --

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 2.2 28.575 -- 0.0 -- 11786 568 94.73 -- 0.1958 0.1942 0.225 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 2.201 2.258 -- 28 515 0.531 0.504 -- 61.77
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 35.1609
Anisotropic B[1][1] 0.11
Anisotropic B[1][2] 0.11
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.11
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.34
RMS Deviations
Key Refinement Restraint Deviation
r_angle_refined_deg 1.319
r_mcbond_other 2.404
r_mcbond_it 2.454
r_mcangle_it 3.882
r_dihedral_angle_2_deg 34.979
r_dihedral_angle_4_deg 15.092
r_chiral_restr 0.079
r_dihedral_angle_3_deg 13.712
r_bond_refined_d 0.013
r_angle_other_deg 0.849
r_dihedral_angle_1_deg 6.472
r_bond_other_d 0.002
r_gen_planes_other 0.001
r_gen_planes_refined 0.005
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1335
Nucleic Acid Atoms 0
Heterogen Atoms 23
Solvent Atoms 70

Software

Software
Software Name Purpose
MolProbity model building version: 3beta29
PDB_EXTRACT data extraction version: 3.10
PHASER phasing version: 2.3.0
XSCALE data scaling version: March 15, 2012
REFMAC refinement version: 5.7.0032
XDS data reduction