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Crystal Structure of Cytochrome P450 (CYP101D5)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NV5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIQUID DIFFUSION 293 1.6 M ammonium phosphate monobasic
Crystal Properties Matthews coefficient Solvent content 2.33 47.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.524 α = 90 b = 109.573 β = 90 c = 113.878 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 EIGER X 9M 2021-09-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 5C (4A) 1 PAL/PLS 5C (4A)
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 3.2 43.79 99.4 1 10.1 4.6 14555 92.37
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 3.2 3.31 0.529
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3NV5 3.2 43.79 1.35 14507 1443 98.92 0.268 0.2624 0.2625 0.319 0.3191 88.19
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 f_dihedral_angle_d 11.9546 f_angle_d 0.5478 f_chiral_restr 0.0429 f_plane_restr 0.0045 f_bond_d 0.0023
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6254 Nucleic Acid Atoms Solvent Atoms 13 Heterogen Atoms 86
Software Software Software Name Purpose Blu-Ice data collection PHENIX refinement Blu-Ice data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing