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Crystal structure of cytochrome P450 NasF5053 S284A-V288A mutant variant from Streptomyces sp. NRRL F-5053 in the cyclo-L-Trp-L-Pro-bound state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6VXV PDB entry 6VXV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.2 M calcium chloride, 20% w/v PEG3350
Crystal Properties Matthews coefficient Solvent content 2.07 40.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.236 α = 90 b = 91.208 β = 90 c = 93.46 γ = 90
Symmetry Space Group P 2 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 16M 2019-08-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.954 Australian Synchrotron MX2
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 1.68 46.73 98.4 0.118 0.128 0.049 0.998 12.1 6.7 41405 14.82
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 1.68 1.71 1.041 1.128 0.429 0.744 1.8
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 PDB entry 6VXV 1.68 46.73 1.34 41363 1974 98.04 0.1708 0.1691 0.17 0.2032 0.2041 19.56
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 23.9678 f_angle_d 1.207 f_chiral_restr 0.0582 f_bond_d 0.0102 f_plane_restr 0.0076
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3017 Nucleic Acid Atoms Solvent Atoms 342 Heterogen Atoms 86
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHENIX phasing PHENIX model building