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Crystal structure of the P450 domain of the CYP51-ferredoxin fusion protein from Methylococcus capsulatus, ligand-free state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6MCW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 291 Potassium phosphate, PEG 3350, glycerol
Crystal Properties Matthews coefficient Solvent content 4.33 71.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 151.861 α = 90 b = 151.861 β = 90 c = 67.246 γ = 120
Symmetry Space Group P 31 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 300 mm CCD 2018-05-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall 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 2.73 65.84 97.6 0.055 16 5.3 24087
Highest Resolution Shell 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 2.73 2.8 99.9 0.8 1.2 5.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 6MCW 2.73 65.84 22239 1269 97.6 0.21502 0.21396 0.2211 0.23426 0.235 RANDOM 83.677
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] -1.58 -0.79 -1.58 5.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.368 r_dihedral_angle_4_deg 18.243 r_long_range_B_other 17.841 r_long_range_B_refined 17.83 r_dihedral_angle_3_deg 17.229 r_scangle_other 12.259 r_mcangle_it 11.033 r_mcangle_other 11.031 r_scbond_it 8.273 r_scbond_other 8.272
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.368 r_dihedral_angle_4_deg 18.243 r_long_range_B_other 17.841 r_long_range_B_refined 17.83 r_dihedral_angle_3_deg 17.229 r_scangle_other 12.259 r_mcangle_it 11.033 r_mcangle_other 11.031 r_scbond_it 8.273 r_scbond_other 8.272 r_mcbond_it 7.715 r_mcbond_other 7.714 r_dihedral_angle_1_deg 7.312 r_angle_refined_deg 1.103 r_angle_other_deg 1.072 r_chiral_restr 0.038 r_gen_planes_refined 0.005 r_bond_refined_d 0.002 r_gen_planes_other 0.001 r_bond_other_d r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3609 Nucleic Acid Atoms Solvent Atoms 79 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing