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Crystal structure of Cytochrome P450 107P2 from streptomyces avermitilis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7WEX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 288.15 17.5% PEG 3350, 0.2M Magnesium acetate tetrahydrate, pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.4 48.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.128 α = 90 b = 66.44 β = 90 c = 111.756 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 288.15 PIXEL DECTRIS PILATUS3 6M 2023-07-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 11C 0.979 PAL/PLS 11C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) 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 1.986 44.209 99.8 1.88 1.2 12.6 31112
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.986 5.1791 0.997
Refinement Statistics 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 (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.986 44.209 30653 1466 98.528 0.225 0.2227 0.2294 0.2721 0.2769 37.27
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] -0.512 -0.98 1.493
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.883 r_dihedral_angle_4_deg 22.968 r_dihedral_angle_3_deg 20.079 r_lrange_it 7.661 r_lrange_other 7.659 r_dihedral_angle_1_deg 5.464 r_scangle_it 4.476 r_scangle_other 4.475 r_mcangle_it 3.928 r_mcangle_other 3.927
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.883 r_dihedral_angle_4_deg 22.968 r_dihedral_angle_3_deg 20.079 r_lrange_it 7.661 r_lrange_other 7.659 r_dihedral_angle_1_deg 5.464 r_scangle_it 4.476 r_scangle_other 4.475 r_mcangle_it 3.928 r_mcangle_other 3.927 r_scbond_it 2.979 r_scbond_other 2.978 r_mcbond_it 2.739 r_mcbond_other 2.735 r_angle_refined_deg 1.463 r_angle_other_deg 1.361 r_symmetry_xyhbond_nbd_refined 0.645 r_nbd_refined 0.221 r_symmetry_nbd_refined 0.205 r_nbd_other 0.202 r_symmetry_nbd_other 0.197 r_nbtor_refined 0.167 r_xyhbond_nbd_refined 0.148 r_symmetry_nbtor_other 0.081 r_symmetry_xyhbond_nbd_other 0.072 r_chiral_restr 0.071 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2985 Nucleic Acid Atoms Solvent Atoms 51 Heterogen Atoms 49
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing