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Crystal structure of dipicolinate synthase, A chain, from Bacillus subtilis
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 294 0.2 M Lithium sulfate, 0.1 M Tris buffer, 25% PEG 3350, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 3.29 62.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 261.578 α = 90 b = 75.108 β = 119.74 c = 200.464 γ = 90
Symmetry Space Group C 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 CCD SBC-2 2003-07-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97920 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 2.79 40 97 0.146 5.5 81355 81355 61.3
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 2.79 2.9 88.6 0.774 1.37 7396
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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 THROUGHOUT 2.79 40 81346 81346 4079 96.38 0.2011 0.2011 0.1986 0.1926 0.2494 0.2425 RANDOM 35.904
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] 0.7 -1.27 -1.19 -0.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.811 r_dihedral_angle_3_deg 23.213 r_dihedral_angle_4_deg 22.557 r_dihedral_angle_1_deg 5.954 r_scangle_it 2.223 r_angle_refined_deg 1.57 r_scbond_it 1.333 r_mcangle_it 0.939 r_mcbond_it 0.565 r_nbtor_refined 0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.811 r_dihedral_angle_3_deg 23.213 r_dihedral_angle_4_deg 22.557 r_dihedral_angle_1_deg 5.954 r_scangle_it 2.223 r_angle_refined_deg 1.57 r_scbond_it 1.333 r_mcangle_it 0.939 r_mcbond_it 0.565 r_nbtor_refined 0.32 r_symmetry_vdw_refined 0.266 r_nbd_refined 0.244 r_symmetry_hbond_refined 0.189 r_xyhbond_nbd_refined 0.15 r_chiral_restr 0.11 r_bond_refined_d 0.013 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 17942 Nucleic Acid Atoms Solvent Atoms 121 Heterogen Atoms 391
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction SBC-Collect data collection HKL-2000 data reduction SHELXD phasing SOLVE phasing RESOLVE phasing HKL-2000 data scaling