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Crystal structure of Cytochrome P450 GymB5 from Streptomyces katrae in complex with cYY and Hypoxanthine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1N40
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277 20 mM sodium formate, 20 mM ammonium acetate, 20 mM sodium citrate, 20 mM potassium sodium tartrate, 20 mM sodium oxamate, 13% MPD, 13% PEG 1000, 13% PEG3350, 100 mM BIS-Tris pH 8.7, 1.25% DMSO
Crystal Properties Matthews coefficient Solvent content 2.59 52.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.83 α = 90 b = 95.482 β = 108.28 c = 79.451 γ = 90
Symmetry Space Group P 1 21 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 PIXEL DECTRIS EIGER X 16M 2023-03-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) CC (Half) 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 1.8 49.02 99.8 0.13 0.99 10.3 5 83878
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 1.81 1.92 0.64
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 (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 1.81 41.72 82200 1678 99.85 0.18557 0.18494 0.1927 0.21633 0.2247 RANDOM 30.883
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] 0.37 -0.47 -1.77 1.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.024 r_dihedral_angle_4_deg 18.213 r_dihedral_angle_3_deg 13.914 r_long_range_B_refined 7.165 r_long_range_B_other 7.137 r_dihedral_angle_1_deg 6.288 r_scangle_other 3.411 r_scbond_other 2.467 r_scbond_it 2.466 r_mcangle_it 2.023
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.024 r_dihedral_angle_4_deg 18.213 r_dihedral_angle_3_deg 13.914 r_long_range_B_refined 7.165 r_long_range_B_other 7.137 r_dihedral_angle_1_deg 6.288 r_scangle_other 3.411 r_scbond_other 2.467 r_scbond_it 2.466 r_mcangle_it 2.023 r_mcangle_other 2.023 r_angle_refined_deg 1.704 r_angle_other_deg 1.43 r_mcbond_it 1.3 r_mcbond_other 1.299 r_chiral_restr 0.088 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_gen_planes_other 0.003 r_bond_other_d 0.001 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 5922 Nucleic Acid Atoms Solvent Atoms 554 Heterogen Atoms 152
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing