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Substrate-free structure of CYP105AW5 from deep-sea Streptomyces aculeolatus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.06 M divalent cations (0.3 M magnesium chloride hexahydrate and 0.3 M calcium chloride dehydrate), 0.1 M Buffer system 2 (1 M sodium HEPES and MOPS, pH 7.5) and 50% (v/v) Precipitant Mix 1 [40% (v/v) PEG 500 MME and 20% (w/v) PEG 20000
Crystal Properties Matthews coefficient Solvent content 2.81 56.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.84 α = 90 b = 140.33 β = 90 c = 48.05 γ = 90
Symmetry Space Group P 21 21 2
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 PILATUS3 6M 2022-12-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.9785 SSRF BL18U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.69 40.59 99.8 0.999 16.9 12.8 58251
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 1.69 1.73 0.756
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 1.69 40.59 54863 1945 97.38 0.16843 0.16724 0.1754 0.20142 0.204 RANDOM 23.679
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] -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.496 r_dihedral_angle_4_deg 18.68 r_dihedral_angle_3_deg 12.882 r_long_range_B_refined 7.048 r_long_range_B_other 6.899 r_dihedral_angle_1_deg 5.792 r_scangle_other 5.788 r_scbond_it 3.875 r_scbond_other 3.874 r_mcangle_other 3.028
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.496 r_dihedral_angle_4_deg 18.68 r_dihedral_angle_3_deg 12.882 r_long_range_B_refined 7.048 r_long_range_B_other 6.899 r_dihedral_angle_1_deg 5.792 r_scangle_other 5.788 r_scbond_it 3.875 r_scbond_other 3.874 r_mcangle_other 3.028 r_mcangle_it 3.025 r_mcbond_it 2.137 r_mcbond_other 2.128 r_angle_refined_deg 1.842 r_angle_other_deg 1.508 r_chiral_restr 0.102 r_bond_refined_d 0.014 r_gen_planes_refined 0.011 r_gen_planes_other 0.006 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 3195 Nucleic Acid Atoms Solvent Atoms 505 Heterogen Atoms 71
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHENIX phasing