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Crystal structure of particulate methane monooxygenase from Methylocystis sp. ATCC 49242 (Rockwell)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3RFR PDB entry 3RFR
Crystallization Crystalization Experiments 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 Matthews coefficient Solvent content 3 58.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.462 α = 90 b = 184.531 β = 90 c = 189.417 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment 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 ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.37765 APS 23-ID-D
Data Collection Overall 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 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 (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) 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 0.2347 0.2887 0.2856 RANDOM 42.225
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] -0.3 0.92 -0.61
RMS Deviations 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 Non-Hydrogen Atoms Number Protein Atoms 20526 Nucleic Acid Atoms Solvent Atoms 117 Heterogen Atoms 211
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction