☰ Navigation Tabs
Crystal structure of dipicolinate synthase subunit B from Bacillus halodurans C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 291 0.1 M Tris, 0.3 M 195NSBD, 2.0 M Ammonium dihydrogen phosphate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.79 55.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.185 α = 90 b = 110.185 β = 90 c = 71.35 γ = 120
Symmetry Space Group P 63 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315r mirrors 2010-02-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.9794 APS 19-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 2.1 40 96.8 0.11 20.5 5.5 15060 14994 2 2 40
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 2.1 2.14 99.7 0.64 2.8 5.4 742
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 SAD THROUGHOUT 2.1 40 2 2 14930 14181 749 96.88 0.17 0.16882 0.16658 0.181 0.21296 0.2137 RANDOM 15.038
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] 0.21 0.1 0.21 -0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.549 r_dihedral_angle_4_deg 19.912 r_dihedral_angle_3_deg 14.202 r_dihedral_angle_1_deg 6.421 r_scangle_it 5.541 r_scbond_it 3.245 r_mcangle_it 2.021 r_angle_refined_deg 1.781 r_mcbond_it 1.094 r_angle_other_deg 1.077
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.549 r_dihedral_angle_4_deg 19.912 r_dihedral_angle_3_deg 14.202 r_dihedral_angle_1_deg 6.421 r_scangle_it 5.541 r_scbond_it 3.245 r_mcangle_it 2.021 r_angle_refined_deg 1.781 r_mcbond_it 1.094 r_angle_other_deg 1.077 r_mcbond_other 0.301 r_chiral_restr 0.123 r_bond_refined_d 0.023 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1460 Nucleic Acid Atoms Solvent Atoms 84 Heterogen Atoms 10
Software Software Software Name Purpose SBC-Collect data collection HKL-3000 phasing DM model building SHELX model building MLPHARE phasing Coot model building ARP/wARP model building REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling DM phasing SHELX phasing