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Substrate-bound crystal structure of a P450 enzyme DmlH that catalyze intramolecular phenol coupling in the biosynthesis of cihanmycins
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other unreported crystal structure
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 289 3 M CaCl2, 0.3 M MgCl2, 0.5 M MES, 0.5 M imidazole, 37.5% w/v PEG 1K_PEG 3350_MPD, pH 6.5
Crystal Properties Matthews coefficient Solvent content 1.99 38.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.082 α = 90 b = 100.162 β = 90 c = 105.811 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 PILATUS 200K 2023-06-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
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 2.2 19.68 99.9 0.095 0.101 0.032 0.998 15.8 9.3 20263
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 2.32 100 0.49 0.548 0.24 0.828 5
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 2.2 19.68 1.34 20211 949 99.98 0.1854 0.183 0.1825 0.2336 0.2348
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 9.07 f_angle_d 0.934 f_chiral_restr 0.052 f_plane_restr 0.014 f_bond_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3041 Nucleic Acid Atoms Solvent Atoms 193 Heterogen Atoms 150
Software Software Software Name Purpose PHENIX refinement Aimless data scaling MOLREP phasing CrysalisPro data reduction