4PHZ
Crystal structure of particulate methane monooxygenase from Methylocystis sp. ATCC 49242 (Rockwell)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3RFR | PDB entry 3RFR |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 295 | 10% PEG3000, 0.1 M sodium cacodylate trihydrate, pH 6.5, 0.2 M magnesium formate |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3 | 58.99 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 117.462 | α = 90 |
b = 184.531 | β = 90 |
c = 189.417 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 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 | 110 | CCD | MARMOSAIC 300 mm CCD | 2011-10-16 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 23-ID-D | 1.37765 | APS | 23-ID-D |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 2.59 | 50 | 72.6 | 18.9 | 14.4 | 93278 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | 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 | MOLECULAR REPLACEMENT | THROUGHOUT | PDB entry 3RFR | 2.59 | 50 | 3 | 93278 | 4678 | 72.32 | 0.2393 | 0.2367 | 0.2887 | RANDOM | 42.225 |
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] | |
-0.3 | 0.92 | -0.61 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.004 |
r_dihedral_angle_4_deg | 19.198 |
r_dihedral_angle_3_deg | 19.147 |
r_dihedral_angle_1_deg | 7.631 |
r_angle_refined_deg | 1.666 |
r_chiral_restr | 0.11 |
r_bond_refined_d | 0.012 |
r_gen_planes_refined | 0.006 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 20526 |
Nucleic Acid Atoms | |
Solvent Atoms | 117 |
Heterogen Atoms | 211 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
PDB_EXTRACT | data extraction |