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Androstenedione-bound structure of CYP154C2 from Streptomyces avermitilis in an open conformation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6L69
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 0.06 M Divalents, 0.1 M Buffer System 2 pH 7.5, 50% v/v Precipitant mix 1
Crystal Properties Matthews coefficient Solvent content 3.06 59.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.6 α = 90 b = 80.13 β = 90 c = 120.63 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 298 PIXEL DECTRIS PILATUS 6M 2019-03-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.979 SSRF BL18U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.95 50 100 0.098 0.998 13.5 11.6 39415
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2.06 100 0.932 0.851 2.8 11.5
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 6L69 1.95 49.79 37351 2001 99.99 0.19495 0.19208 0.2 0.2488 0.253 RANDOM 40.571
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.563 r_dihedral_angle_4_deg 20.915 r_dihedral_angle_3_deg 15.046 r_long_range_B_other 8.154 r_long_range_B_refined 8.151 r_dihedral_angle_1_deg 6.428 r_scangle_other 6.343 r_mcangle_it 5.077 r_mcangle_other 5.076 r_scbond_it 4.326
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.563 r_dihedral_angle_4_deg 20.915 r_dihedral_angle_3_deg 15.046 r_long_range_B_other 8.154 r_long_range_B_refined 8.151 r_dihedral_angle_1_deg 6.428 r_scangle_other 6.343 r_mcangle_it 5.077 r_mcangle_other 5.076 r_scbond_it 4.326 r_scbond_other 4.324 r_mcbond_it 3.698 r_mcbond_other 3.696 r_angle_refined_deg 1.62 r_angle_other_deg 1.369 r_chiral_restr 0.077 r_bond_refined_d 0.01 r_gen_planes_other 0.01 r_gen_planes_refined 0.009 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 3017 Nucleic Acid Atoms Solvent Atoms 304 Heterogen Atoms 71
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction iMOSFLM data reduction SCALA data scaling MOLREP phasing