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Crystal Structure of FosB from Bacillus cereus with Zinc and (1-hydroxypropan-2-yl)phosphonic 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 298 Protein solution (10 mg/mL FosB in 20 mM HEPES buffer, pH 7.5 and 5 mM inhibitor) and reservoir solution (75 mM Mg formate and 14% (w/v) PEG 3350) were mixed in a Hampton Research VDX plate using a 2:3 ratio of protein:reservoir solutions. Cryoprotected in its reservoir solution with 20% glycerol added prior to rapid freezing in liquid nitrogen
Crystal Properties Matthews coefficient Solvent content 2.29 46.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.233 α = 90 b = 68.21 β = 90 c = 69.826 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 2022-09-26 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) 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 1.81 50 99.9 0.138 0.145 0.044 0.994 4.1 10.7 28683
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 1.81 1.84 100 0.785 0.829 0.263 0.841 9.5
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4JH6 1.81 48.793 28626 1462 99.725 0.156 0.1543 0.167 0.1852 0.1952 RANDOM 19.454
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] 0.002 -0.004 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.519 r_dihedral_angle_3_deg 13.282 r_dihedral_angle_1_deg 6.897 r_lrange_it 6.454 r_lrange_other 6.342 r_dihedral_angle_2_deg 5.582 r_scangle_it 4.495 r_scangle_other 4.493 r_scbond_it 2.835 r_scbond_other 2.834
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.519 r_dihedral_angle_3_deg 13.282 r_dihedral_angle_1_deg 6.897 r_lrange_it 6.454 r_lrange_other 6.342 r_dihedral_angle_2_deg 5.582 r_scangle_it 4.495 r_scangle_other 4.493 r_scbond_it 2.835 r_scbond_other 2.834 r_mcangle_it 2.187 r_mcangle_other 2.187 r_mcbond_it 1.603 r_mcbond_other 1.602 r_angle_refined_deg 1.52 r_angle_other_deg 0.832 r_nbd_refined 0.231 r_symmetry_nbd_refined 0.212 r_symmetry_nbd_other 0.21 r_nbd_other 0.207 r_nbtor_refined 0.193 r_symmetry_xyhbond_nbd_other 0.19 r_xyhbond_nbd_refined 0.163 r_symmetry_xyhbond_nbd_refined 0.158 r_metal_ion_refined 0.115 r_symmetry_nbtor_other 0.084 r_chiral_restr 0.079 r_gen_planes_other 0.012 r_gen_planes_refined 0.009 r_bond_refined_d 0.008 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2324 Nucleic Acid Atoms Solvent Atoms 270 Heterogen Atoms 47
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling PHASER phasing HKL-2000 data reduction