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Substrate-free 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 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 3.04 59.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.98 α = 90 b = 80.04 β = 90 c = 121.13 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 0.085 0.999 17 11.8 39084
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 99.9 0.866 0.897 3.2 12.1
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 49.35 37026 2000 99.93 0.19946 0.19712 0.205 0.24252 0.2447 RANDOM 39.417
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 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.065 r_dihedral_angle_4_deg 15.767 r_dihedral_angle_3_deg 15.452 r_long_range_B_refined 7.943 r_long_range_B_other 7.922 r_dihedral_angle_1_deg 6.515 r_scangle_other 6.041 r_mcangle_it 4.7 r_mcangle_other 4.699 r_scbond_it 4.066
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.065 r_dihedral_angle_4_deg 15.767 r_dihedral_angle_3_deg 15.452 r_long_range_B_refined 7.943 r_long_range_B_other 7.922 r_dihedral_angle_1_deg 6.515 r_scangle_other 6.041 r_mcangle_it 4.7 r_mcangle_other 4.699 r_scbond_it 4.066 r_scbond_other 4.065 r_mcbond_other 3.465 r_mcbond_it 3.464 r_angle_refined_deg 1.639 r_angle_other_deg 1.37 r_chiral_restr 0.079 r_bond_refined_d 0.009 r_gen_planes_other 0.009 r_gen_planes_refined 0.008 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 3016 Nucleic Acid Atoms Solvent Atoms 310 Heterogen Atoms 57
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction iMOSFLM data reduction SCALA data scaling MOLREP phasing