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Crystal structure of cyclo-L-Trp-L-Pro-bound cytochrome P450 NasF5053 from Streptomyces sp. NRRL F-5053
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ABB PDB entry 3ABB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 0.2 M calcium chloride, 20% w/v PEG3350
Crystal Properties Matthews coefficient Solvent content 2.09 41.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.314 α = 90 b = 91.836 β = 90 c = 93.604 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 2019-08-15 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 1.6 46.8 99.9 0.085 0.092 0.036 0.99 11.8 6.7 48951 19.96
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 1.6 1.63 99.7 1.177 1.271 0.476 0.709 1.7 6.9
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE PDB entry 3ABB 1.6 46.8 1.34 48877 2431 99.73 0.1712 0.1696 0.1706 0.2034 0.2038 Random selection of 5% diffraction data 26.8
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 16.0469 f_angle_d 0.9311 f_chiral_restr 0.0535 f_bond_d 0.0052 f_plane_restr 0.0048
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3038 Nucleic Acid Atoms Solvent Atoms 351 Heterogen Atoms 87
Software Software Software Name Purpose PHENIX refinement Blu-Ice data collection XDS data reduction Aimless data scaling PHASER phasing PHENIX model building