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Crystal structure of cytochrome P450 IkaD from Streptomyces sp. ZJ306, in complex with the substrate 10-epi-maltophilin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other a crystal structure of IkaD in complex with 10-epi-deOH-HSAF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 289 3.5-4 M sodium formate
Crystal Properties Matthews coefficient Solvent content 2.94 58.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.895 α = 90 b = 81.948 β = 94.3 c = 143.838 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 2019-11-27 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 13.29 99.2 0.162 0.182 0.08 0.986 7.8 4.9 71321
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 2.04 97.7 0.647 0.801 0.463 0.538 2.7
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 13.29 1.34 71307 3618 99.45 0.1912 0.189 0.1895 0.2331 0.2331
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 8.264 f_angle_d 1.335 f_chiral_restr 0.059 f_bond_d 0.012 f_plane_restr 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6098 Nucleic Acid Atoms Solvent Atoms 847 Heterogen Atoms 173
Software Software Software Name Purpose PHENIX refinement Aimless data scaling CrysalisPro data reduction MOLREP phasing