X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.75
Temperature 298.0
Details Protein solution: 45 mg/mL protein in 10 mM NaCl and 10 mM Tris-HCl, 2.5 mM methylmalonyl-CoA, pH 8.0. Precipitant solution: 12 - 18% glycerol, 1.3 - 1.6 M (NH4)2SO4, 0.1 M Tris-HCl, pH 7.0 - 8.5 (1:1, protein:well), VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 60.17 α = 90
b = 60.17 β = 90
c = 311.19 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 -- 2009-06-08
Diffraction Radiation
Monochromator Protocol
Si(111) MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 21-ID-D 0.97941, 1.127 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
2.25 28.06 98.8 0.074 -- -- 17.3 17112 16907 -- -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
MAD 2.25 28.06 -- -- 16907 15889 869 100.0 -- 0.20245 0.19977 0.25381 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 2.25 2.308 -- 67 1147 0.196 0.266 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 23.1
Anisotropic B[1][1] 0.01
Anisotropic B[1][2] 0.01
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.01
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.02
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 2.606
r_scbond_it 1.625
r_mcangle_it 1.098
r_mcbond_it 0.573
r_gen_planes_refined 0.005
r_chiral_restr 0.082
r_dihedral_angle_4_deg 16.91
r_dihedral_angle_3_deg 14.211
r_dihedral_angle_2_deg 34.695
r_dihedral_angle_1_deg 6.077
r_angle_refined_deg 1.233
r_bond_refined_d 0.009
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2340
Nucleic Acid Atoms 0
Heterogen Atoms 39
Solvent Atoms 113

Software

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