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Crystal structure of ferredoxin/flavodoxin NADP+ oxidoreductase 1 (FNR1) V329H mutant from Bacillus cereus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6GAR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 298 42 mg/mL protein (1:1) 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD, 0.02 M sodium formate, 0.02 M ammonium acetate, 0.02 M trisodium citrate, 0.02 M sodium potassium l-tartrate, 0.02 M sodium oxamate, 0.1 M MOPS/HEPES-Na pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.86 57.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 164.612 α = 90 b = 56.935 β = 90 c = 94.388 γ = 90
Symmetry Space Group P 21 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 PIXEL DECTRIS PILATUS3 6M 2021-04-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.976254 ESRF ID30B
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 2.6 53.81 96.1 0.087 0.1 0.049 0.996 8.7 3.7 26835 55.76
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 2.6 2.72 97.6 0.498 0.575 0.281 0.848 2.2 3.6
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 6GAR 2.6 53.81 1.34 26768 1343 95.35 0.1903 0.1878 0.1907 0.2381 0.2389 80.86
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 15.3091 f_angle_d 0.9809 f_chiral_restr 0.0598 f_bond_d 0.0084 f_plane_restr 0.0065
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5402 Nucleic Acid Atoms Solvent Atoms 59 Heterogen Atoms 122
Software Software Software Name Purpose PHENIX refinement REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing