3M2U
Structural Insight into Methyl-Coenzyme M Reductase Chemistry using Coenzyme B Analogues
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 282 | PEG 400, magnesium acetate, vapor diffusion, sitting drop, temperature 282K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.18 | 43.47 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 82.016 | α = 90 |
b = 118.26 | β = 91.84 |
c = 122.387 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | ADSC QUANTUM 315 | 2007-12-08 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 14-BM-C | 0.90020 | APS | 14-BM-C |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge 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 | 1.4 | 50 | 99.9 | 0.073 | 20.389 | 5.4 | 446793 | 446253 | 1 | 3 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.4 | 1.45 | 100 | 0.447 | 4.029 | 5.4 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | FOURIER SYNTHESIS | THROUGHOUT | 1.4 | 19.89 | 452782 | 423854 | 22348 | 98.55 | 0.13163 | 0.13037 | 0.1553 | RANDOM | 14.57 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
0.06 | 0.06 | 0.59 | -0.65 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.685 |
r_dihedral_angle_4_deg | 15.916 |
r_dihedral_angle_3_deg | 12.881 |
r_dihedral_angle_1_deg | 6.38 |
r_scangle_it | 4.897 |
r_scbond_it | 3.056 |
r_angle_refined_deg | 2.625 |
r_mcangle_it | 1.947 |
r_mcbond_it | 1.25 |
r_chiral_restr | 0.195 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 19098 |
Nucleic Acid Atoms | |
Solvent Atoms | 2290 |
Heterogen Atoms | 282 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
BioCARS-developed | data collection |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
REFMAC | phasing |