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Multifunctional cytochrome P450 enzyme IkaD from Streptomyces sp. ZJ306, in complex with epoxyikarugamycin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other 8JOO structure of IkaD in complex with ikarugamycin
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 289 3.5-4M sodium formate
Crystal Properties Matthews coefficient Solvent content 2.84 56.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.6201 α = 90 b = 81.9395 β = 94.3858 c = 144.165 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 2020-01-15 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 23.310357633 99.7 0.103 0.115 0.049 0.994 10.5 5.1 72440 19.6584059616
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 99.5 0.638 0.775 0.432 0.544 3
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 2.00001111553 23.310357633 1.33702057403 72430 3659 99.7054126975 0.206499818957 0.203840751972 0.2074 0.255652344084 0.2585 27.6442843374
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 14.8410722406 f_angle_d 1.4734066863 f_chiral_restr 0.292470168004 f_bond_d 0.0140028608976 f_plane_restr 0.00828246346957
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6093 Nucleic Acid Atoms Solvent Atoms 747 Heterogen Atoms 182
Software Software Software Name Purpose PHENIX refinement Aimless data scaling CrysalisPro data reduction MOLREP phasing