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Crystal Structure of metal-dependent hydrolase complexed with manganese from Bacillus smithii
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1R61
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.2 293 35% 2-ethoxyethanol, 0.1 M Na/K phosphate buffer pH 6.2, 0.2 M NaCl
Crystal Properties Matthews coefficient Solvent content 2.31 46.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.21 α = 90 b = 70.198 β = 105.77 c = 104.839 γ = 90
Symmetry Space Group P 1 2 1
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 PILATUS 2M 2022-11-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 0.9800 Photon Factory BL-17A
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 2.53 44.91 97.3 0.101 0.121 0.066 0.952 8.2 3.3 41332
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 2.53 2.63 99.9 0.549 0.649 0.343 0.745 2.2 3.5
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 2.53 43.45 39259 2065 97.34 0.2528 0.2503 0.2551 0.2987 0.2973 RANDOM 57.175
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] -0.08 0.09 0.02 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.328 r_dihedral_angle_3_deg 24.504 r_dihedral_angle_4_deg 19.619 r_long_range_B_refined 10.846 r_long_range_B_other 10.829 r_dihedral_angle_1_deg 6.836 r_scangle_other 5.286 r_mcangle_other 5.134 r_mcangle_it 5.133 r_scbond_it 3.168
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.328 r_dihedral_angle_3_deg 24.504 r_dihedral_angle_4_deg 19.619 r_long_range_B_refined 10.846 r_long_range_B_other 10.829 r_dihedral_angle_1_deg 6.836 r_scangle_other 5.286 r_mcangle_other 5.134 r_mcangle_it 5.133 r_scbond_it 3.168 r_scbond_other 3.168 r_mcbond_it 3.162 r_mcbond_other 3.157 r_angle_refined_deg 1.492 r_angle_other_deg 1.249 r_chiral_restr 0.076 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.002 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 9573 Nucleic Acid Atoms Solvent Atoms 329 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing