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Crystal structure of FMN and NADPH-dependent nitroreductase NfnB mutant Y88F derived from sphigopyxis sp. strain HMH
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2WZW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 295 0.1M Tris pH7.0, 40% PEG 300, 8% PEG 1000
Crystal Properties Matthews coefficient Solvent content 2.01 38.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.436 α = 90 b = 90.436 β = 90 c = 101.679 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 270 2020-11-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 0.97933 PAL/PLS 7A (6B, 6C1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.4 50 99.9 0.994 20.2 14 17096 57.6956791201
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.49 0.454
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 2WZW 2.40008728899 33.7873329824 1.336822377 17040 1704 99.818405483 0.192250261313 0.185265108183 0.19 0.256843483919 0.261 68.5171893671
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 17.1834123462 f_angle_d 1.27250027729 f_chiral_restr 0.055258118378 f_bond_d 0.00865918925585 f_plane_restr 0.00646883886198
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3449 Nucleic Acid Atoms Solvent Atoms 9 Heterogen Atoms 62
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling HKL-2000 phasing