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Crystal structure of the CYP154C2 Q230A from Streptomyces avermitilis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7CL9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 The reservoir solution contained a final concentration of 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 2.9 57.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.505 α = 90 b = 79.353 β = 90 c = 116.995 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 100 PIXEL DECTRIS PILATUS 6M 2021-01-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.9785 SSRF BL19U1
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 1.97 50 97.8 0.049 1 28.7 12.3 37350
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 1.97 2 0.832
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.97 39.71 35425 1849 97.53 0.18053 0.17779 0.23439 0.2171 RANDOM 39.54
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 33.762 r_dihedral_angle_4_deg 16.861 r_dihedral_angle_3_deg 13.307 r_long_range_B_refined 7.581 r_long_range_B_other 7.495 r_scangle_other 6.048 r_dihedral_angle_1_deg 5.963 r_mcangle_other 4.148 r_mcangle_it 4.147 r_scbond_it 4.132
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.762 r_dihedral_angle_4_deg 16.861 r_dihedral_angle_3_deg 13.307 r_long_range_B_refined 7.581 r_long_range_B_other 7.495 r_scangle_other 6.048 r_dihedral_angle_1_deg 5.963 r_mcangle_other 4.148 r_mcangle_it 4.147 r_scbond_it 4.132 r_scbond_other 4.131 r_mcbond_it 3.032 r_mcbond_other 3.029 r_angle_refined_deg 1.586 r_angle_other_deg 1.385 r_chiral_restr 0.073 r_gen_planes_other 0.01 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 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 3012 Nucleic Acid Atoms Solvent Atoms 387 Heterogen Atoms 65
Software Software Software Name Purpose REFMAC refinement HKL-3000 data scaling HKL-3000 data reduction MOLREP phasing