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Crystal Structure of FosB from Bacillus cereus with Zinc and Sulfate
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 methylmalonate) and reservoir solution (50 mM Mg formate and 14% (w/v) PEG 3350) were mixed in a Hampton Research VDX plate with 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 46.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.494 α = 90 b = 68.402 β = 90 c = 70.063 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) 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 1.83 50 99.8 0.988 4.3 5.6 27845
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.83 1.86 99.8 0.753 5.4
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 1.83 48.94 26425 1456 99.03 0.1607 0.15923 0.1695 0.18797 0.1988 RANDOM 17.88
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] -0.03 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.656 r_dihedral_angle_4_deg 13.188 r_dihedral_angle_3_deg 11.967 r_dihedral_angle_1_deg 6.742 r_long_range_B_other 5.581 r_long_range_B_refined 5.577 r_scangle_other 3.884 r_scbond_it 2.496 r_scbond_other 2.482 r_angle_other_deg 2.274
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.656 r_dihedral_angle_4_deg 13.188 r_dihedral_angle_3_deg 11.967 r_dihedral_angle_1_deg 6.742 r_long_range_B_other 5.581 r_long_range_B_refined 5.577 r_scangle_other 3.884 r_scbond_it 2.496 r_scbond_other 2.482 r_angle_other_deg 2.274 r_mcangle_it 2.016 r_mcangle_other 2.015 r_angle_refined_deg 1.536 r_mcbond_it 1.432 r_mcbond_other 1.431 r_chiral_restr 0.082 r_bond_other_d 0.035 r_bond_refined_d 0.013 r_gen_planes_other 0.013 r_gen_planes_refined 0.01 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2324 Nucleic Acid Atoms Solvent Atoms 258 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling PHASER phasing HKL-2000 data reduction