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Crystal Structure of FosB from Bacillus cereus with Zinc and Phosphonoacetate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4JH6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 16% PEG 3350, 125 mM magnesium formate, 5 mM phosphonoacetate
Crystal Properties Matthews coefficient Solvent content 2.32 46.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.674 α = 90 b = 67.831 β = 90 c = 69.738 γ = 90
Symmetry Space Group P 21 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 2022-06-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0 APS 22-ID
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 1.975 50 99.8 0.16 0.178 0.077 3.6 5.2 22012
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 1.98 2.01 99.8 0.583 0.652 0.287 0.752 5
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 (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4JH6 1.975 46.808 21965 1049 99.223 0.172 0.1691 0.2204 0.2105 RANDOM 17.79
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] 0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.881 r_dihedral_angle_3_deg 13.531 r_dihedral_angle_2_deg 7.656 r_dihedral_angle_1_deg 6.97 r_lrange_it 4.779 r_lrange_other 4.673 r_scangle_it 3.113 r_scangle_other 3.113 r_scbond_it 1.97 r_scbond_other 1.956
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.881 r_dihedral_angle_3_deg 13.531 r_dihedral_angle_2_deg 7.656 r_dihedral_angle_1_deg 6.97 r_lrange_it 4.779 r_lrange_other 4.673 r_scangle_it 3.113 r_scangle_other 3.113 r_scbond_it 1.97 r_scbond_other 1.956 r_mcangle_it 1.928 r_mcangle_other 1.927 r_angle_refined_deg 1.444 r_mcbond_it 1.296 r_mcbond_other 1.295 r_angle_other_deg 0.779 r_nbd_refined 0.22 r_symmetry_nbd_other 0.21 r_nbd_other 0.196 r_nbtor_refined 0.181 r_xyhbond_nbd_refined 0.155 r_symmetry_nbd_refined 0.149 r_symmetry_xyhbond_nbd_refined 0.131 r_symmetry_nbtor_other 0.084 r_metal_ion_refined 0.079 r_chiral_restr 0.073 r_gen_planes_other 0.01 r_gen_planes_refined 0.008 r_bond_refined_d 0.007 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2326 Nucleic Acid Atoms Solvent Atoms 211 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling PHASER phasing PDB_EXTRACT data extraction HKL-2000 data reduction