8W33
Structure of McrD (methyl-coenzyme M reductase operon protein D) from Methanomassiliicoccus luminyensis
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 279 | MgCl2, CaCl2, MES, imidazole, glycerol, PEG 4000, carboxylic acids mix (formate, acetate, citrate, tartrate, oxamate) |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.04 | 59.5 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 86.062 | α = 90 |
b = 90.224 | β = 90 |
c = 121.415 | γ = 90 |
Symmetry | |
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Space Group | C 2 2 21 |
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 | PIXEL | DECTRIS EIGER X 16M | 2018-12-13 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | AUSTRALIAN SYNCHROTRON BEAMLINE MX2 | 0.95366 | Australian Synchrotron | MX2 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | 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 | 1.65 | 45.15 | 100 | 0.071 | 0.077 | 0.029 | 0.999 | 16.8 | 13.7 | 57078 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 1.65 | 1.68 | 100 | 2.263 | 2.437 | 0.902 | 0.816 | 1.6 | 14 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | SIRAS | FREE R-VALUE | 1.65 | 45.15 | 57036 | 2855 | 99.988 | 0.178 | 0.1776 | 0.1924 | Random Selection | 38.29 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
-1.905 | 3.922 | -2.017 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_6_deg | 15.638 |
r_dihedral_angle_3_deg | 11.722 |
r_lrange_it | 8.133 |
r_lrange_other | 8.084 |
r_dihedral_angle_2_deg | 6.915 |
r_scangle_it | 6.454 |
r_scangle_other | 6.452 |
r_dihedral_angle_1_deg | 6.333 |
r_scbond_it | 4.097 |
r_scbond_other | 4.096 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2275 |
Nucleic Acid Atoms | |
Solvent Atoms | 180 |
Heterogen Atoms | 12 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
Coot | model building |
XDS | data reduction |
Aimless | data scaling |
BUCCANEER | model building |
CRANK2 | phasing |