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Crystal structure of cytochrome P450 IkaD from Streptomyces sp. ZJ306, in complex with the substrate ikarugamycin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8JNO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 289 3.5-4.0 M sodium formate
Crystal Properties Matthews coefficient Solvent content 2.96 58.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.174 α = 90 b = 82.121 β = 94.41 c = 143.92 γ = 90
Symmetry Space Group I 1 2 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 PILATUS 200K 2020-03-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.54184
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 2.25 19.89 97.5 0.159 0.193 0.108 0.977 5 2.8 49517
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 2.25 2.32 98.6 0.418 0.508 0.282 0.79 2.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.25 19.89 1.33 49325 2534 96.97 0.2191 0.2166 0.2172 0.2643 0.2653
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 8.038 f_angle_d 0.875 f_chiral_restr 0.043 f_plane_restr 0.007 f_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6083 Nucleic Acid Atoms Solvent Atoms 643 Heterogen Atoms 175
Software Software Software Name Purpose PHENIX refinement Aimless data scaling CrysalisPro data reduction MOLREP phasing