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Crystal structure of particulate methane monooxygenase from Methylocystis sp. ATCC 49242 (Rockwell) soaked in copper
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 dihydrate
Crystal Properties Matthews coefficient Solvent content 3.33 63.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.361 α = 90 b = 184.739 β = 90 c = 188.637 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 2012-02-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.33765 APS 21-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 3.15 50 77.8 21.5 13.7 55808
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 3.15 50 3 55808 2796 78.21 0.2241 0.2211 0.221 0.2799 0.2793 RANDOM 57.517
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] -0.08 0.52 -0.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.076 r_dihedral_angle_3_deg 20.747 r_dihedral_angle_4_deg 18.661 r_dihedral_angle_1_deg 7.73 r_mcangle_it 7.428 r_scbond_it 4.781 r_mcbond_it 4.536 r_angle_refined_deg 1.683 r_chiral_restr 0.12 r_bond_refined_d 0.012
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.076 r_dihedral_angle_3_deg 20.747 r_dihedral_angle_4_deg 18.661 r_dihedral_angle_1_deg 7.73 r_mcangle_it 7.428 r_scbond_it 4.781 r_mcbond_it 4.536 r_angle_refined_deg 1.683 r_chiral_restr 0.12 r_bond_refined_d 0.012 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 20624 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction