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Crystal structure of Cytochrome P450 GymB5 from Streptomyces katrae
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 tartate, 20 mM sodium oxamate, 13% MPD, 13% PEG 1000, 13% PEG3350, 100 mM BIS-Tris pH 8.7
Crystal Properties Matthews coefficient Solvent content 2.57 52.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.166 α = 90 b = 95.544 β = 109.22 c = 81.459 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 2023-02-11 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 1.9 49.02 99.8 0.12 0.99 10.9 4.8 79072
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 1.91 2.02 0.57
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 1.91 49.02 68841 2130 99.85 0.17096 0.16981 0.1786 0.20818 0.2148 RANDOM 32.3
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] 2.5 -1.03 -1.57 -0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.945 r_dihedral_angle_4_deg 17.52 r_dihedral_angle_3_deg 15.452 r_long_range_B_refined 6.429 r_long_range_B_other 6.401 r_dihedral_angle_1_deg 6.058 r_scangle_other 5.452 r_scbond_other 3.58 r_scbond_it 3.579 r_mcangle_it 3.512
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.945 r_dihedral_angle_4_deg 17.52 r_dihedral_angle_3_deg 15.452 r_long_range_B_refined 6.429 r_long_range_B_other 6.401 r_dihedral_angle_1_deg 6.058 r_scangle_other 5.452 r_scbond_other 3.58 r_scbond_it 3.579 r_mcangle_it 3.512 r_mcangle_other 3.512 r_mcbond_other 2.551 r_mcbond_it 2.55 r_angle_refined_deg 1.587 r_angle_other_deg 1.42 r_chiral_restr 0.08 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_gen_planes_other 0.003 r_bond_other_d 0.002 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 5888 Nucleic Acid Atoms Solvent Atoms 505 Heterogen Atoms 86
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing