X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 298.0
Details Protein: 20 mg/mL in 100 mM NaCl and 10 mM Tris-HCl, pH 8.0 plus 10 mM methylmalonyl-CoA. Precipitant: 20 - 23% MEPEG 2000, 0.25-0.35 M (NH4)2SO4 and 0.1 M Bis-tris propane-HCl, pH 7.0 in 4 L drops (1:1, protein:well), VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 60.49 α = 90
b = 60.49 β = 90
c = 310.96 γ = 120
Symmetry
Space Group P 61 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD -- 2009-12-10
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 21-ID-G 0.97872 APS 21-ID-G

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
1.76 26.12 97.7 0.094 -- -- 9.4 35241 34431 -- -3.0 --

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
-- 1.76 25.39 -- -- -- 32400 1717 98.44 -- 0.22161 0.2201 0.24929 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 1.763 1.809 -- 113 2297 0.364 0.376 -- 97.37
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 34.132
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_scangle_it 5.313
r_scbond_it 3.347
r_mcangle_it 2.362
r_mcbond_it 1.429
r_gen_planes_refined 0.011
r_chiral_restr 0.158
r_dihedral_angle_4_deg 18.748
r_dihedral_angle_3_deg 16.169
r_dihedral_angle_2_deg 35.421
r_dihedral_angle_1_deg 7.04
r_angle_refined_deg 2.127
r_bond_refined_d 0.024
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2346
Nucleic Acid Atoms 0
Heterogen Atoms 27
Solvent Atoms 98

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL-2000 Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
REFMAC 5.5.0109 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.5.0109 refinement
HKL-2000 data collection