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High-resolution crystal structure of Vibrio cholerae NFeoB in the apo form in orthorhombic space group
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8VWL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 1.4 M lithium sulfate, 0.1 M HEPES sodium, pH 7.2, 2 % (v/v) trifluoroethane
Crystal Properties Matthews coefficient Solvent content 3.17 61.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.483 α = 90 b = 101.106 β = 90 c = 301.61 γ = 90
Symmetry Space Group C 2 2 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 2025-02-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-2 0.97935 NSLS-II 17-ID-2
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 1.85 43.53 100 0.997 10.2 14 125249
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 1.85 1.88 0.373
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.85 43.53 118785 6463 99.94 0.17761 0.17599 0.1859 0.20728 0.2177 RANDOM 38.347
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] -1.03 -2.57 3.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.725 r_long_range_B_other 12.732 r_long_range_B_refined 12.697 r_scangle_other 11.572 r_scbond_it 9.753 r_scbond_other 9.26 r_dihedral_angle_1_deg 6.284 r_mcangle_it 4.74 r_mcangle_other 4.74 r_mcbond_it 3.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.725 r_long_range_B_other 12.732 r_long_range_B_refined 12.697 r_scangle_other 11.572 r_scbond_it 9.753 r_scbond_other 9.26 r_dihedral_angle_1_deg 6.284 r_mcangle_it 4.74 r_mcangle_other 4.74 r_mcbond_it 3.68 r_mcbond_other 3.678 r_angle_refined_deg 1.428 r_angle_other_deg 0.507 r_chiral_restr 0.073 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8118 Nucleic Acid Atoms Solvent Atoms 848 Heterogen Atoms 208
Software Software Software Name Purpose REFMAC refinement AutoProcess data reduction AutoProcess data scaling AutoProcess phasing