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Crystal structure of sterol 14 alpha-demethylase (CYP51) from deep-sea fish Coryphaenoides armatus (abyssal grenadier) in the ligand-free state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8SBI ligand-free
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.7 291 PEG 3350, Magnesium Acetate, Tetradecyl-b-D-maaltoside
Crystal Properties Matthews coefficient Solvent content 2.24 45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.596 α = 90 b = 63.135 β = 97.59 c = 104.86 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 9M 2024-02-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.9677 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 2.9 29.09 96.9 0.075 0.082 0.035 1 27 5.9 18679 79
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.9 2.97 98.1 0.726 0.799 0.328 0.786 2.5 5.4
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 2.9 29.09 18679 996 96.92 0.2329 0.23173 0.24817 0.243 RANDOM 98.001
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] -2.47 -3.66 2.67 0.74
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_other 16.591 r_long_range_B_refined 16.59 r_dihedral_angle_3_deg 15.801 r_scangle_other 11.755 r_mcangle_it 11.518 r_mcangle_other 11.517 r_scbond_other 7.523 r_scbond_it 7.522 r_mcbond_it 7.466 r_mcbond_other 7.466
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_other 16.591 r_long_range_B_refined 16.59 r_dihedral_angle_3_deg 15.801 r_scangle_other 11.755 r_mcangle_it 11.518 r_mcangle_other 11.517 r_scbond_other 7.523 r_scbond_it 7.522 r_mcbond_it 7.466 r_mcbond_other 7.466 r_dihedral_angle_1_deg 5.504 r_dihedral_angle_2_deg 3.781 r_angle_refined_deg 1.063 r_angle_other_deg 0.37 r_chiral_restr 0.051 r_gen_planes_refined 0.005 r_bond_refined_d 0.004 r_gen_planes_other 0.004 r_bond_other_d 0.001 r_dihedral_angle_4_deg 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 7019 Nucleic Acid Atoms Solvent Atoms 22 Heterogen Atoms 86
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing