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Crystal Structure of FosB from Bacillus cereus with Zinc and 2-Phosphonopropionic acid
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 2-phosphonopropionic acid
Crystal Properties Matthews coefficient Solvent content 2.32 46.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.314 α = 90 b = 68.016 β = 90 c = 69.802 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 1.9 50 97.6 0.141 0.158 0.069 3.7 5 24190
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 1.9 1.93 98.3 0.57 0.634 0.274 0.775 5.1
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4JH6 1.9 38.832 24142 1092 97.524 0.171 0.1693 0.1796 0.2188 0.2235 RANDOM 17.204
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] 0.005 -0.004 -0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.699 r_dihedral_angle_3_deg 13.193 r_dihedral_angle_1_deg 6.845 r_dihedral_angle_2_deg 6.136 r_lrange_it 5.389 r_lrange_other 5.291 r_scangle_it 3.49 r_scangle_other 3.489 r_mcangle_it 2.568 r_mcangle_other 2.567
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.699 r_dihedral_angle_3_deg 13.193 r_dihedral_angle_1_deg 6.845 r_dihedral_angle_2_deg 6.136 r_lrange_it 5.389 r_lrange_other 5.291 r_scangle_it 3.49 r_scangle_other 3.489 r_mcangle_it 2.568 r_mcangle_other 2.567 r_scbond_it 2.213 r_scbond_other 2.212 r_mcbond_it 1.732 r_mcbond_other 1.72 r_angle_refined_deg 1.489 r_angle_other_deg 0.805 r_nbd_refined 0.229 r_symmetry_nbd_refined 0.229 r_nbd_other 0.219 r_symmetry_nbd_other 0.209 r_nbtor_refined 0.181 r_xyhbond_nbd_refined 0.155 r_symmetry_xyhbond_nbd_refined 0.154 r_symmetry_nbtor_other 0.085 r_chiral_restr 0.077 r_symmetry_xyhbond_nbd_other 0.076 r_metal_ion_refined 0.076 r_gen_planes_other 0.011 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2326 Nucleic Acid Atoms Solvent Atoms 218 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling PHASER phasing PDB_EXTRACT data extraction HKL-2000 data reduction