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Crystal Structure of the Flavoprotein NrdI from Aerococcus urinae in Oxidized Form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3N3A 3N3A, chain C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 298 17% (w/v) PEG 20000, 0.1 M sodium acetate pH 4.6
Crystal Properties Matthews coefficient Solvent content 2.31 46.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.444 α = 90 b = 50.057 β = 112.57 c = 64.272 γ = 90
Symmetry Space Group P 1 21 1
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 RAYONIX MX-300 2018-02-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.95 59.35 97.4 0.034 0.037 0.013 14 7.5 23129
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 1.95 1.98 95.1 0.404 0.437 0.165 0.953 6.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 THROUGHOUT 3N3A, chain C 1.95 59.35 21480 1082 94.81 0.2399 0.2384 0.2443 0.2692 0.2725 RANDOM 26.277
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] -0.23 -0.15 0.44 -0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.841 r_dihedral_angle_4_deg 18.253 r_dihedral_angle_3_deg 13.093 r_dihedral_angle_1_deg 5.861 r_angle_refined_deg 1.182 r_angle_other_deg 0.863 r_chiral_restr 0.066 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.841 r_dihedral_angle_4_deg 18.253 r_dihedral_angle_3_deg 13.093 r_dihedral_angle_1_deg 5.861 r_angle_refined_deg 1.182 r_angle_other_deg 0.863 r_chiral_restr 0.066 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2071 Nucleic Acid Atoms Solvent Atoms 75 Heterogen Atoms 62
Software Software Software Name Purpose HKL-2000 data reduction HKL-2000 data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction