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Crystal structure of dihydrodipicolinate synthase from Agrobacterium tumefaciens str. C58
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 0.2M Mg formate, 20% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.35 47.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.116 α = 79.35 b = 49.442 β = 89.06 c = 69.084 γ = 83.94
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 315 Mirrors 2006-10-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97940 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 1.2 67.88 93.19 0.077 17.89 4.7 169533 157988 2 9.8
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 1.2 1.231 72.49 0.274 3 3 13239
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 SAD THROUGHOUT 1.2 67.88 157988 157988 8360 93.19 0.12846 0.12846 0.12703 0.1249 0.15559 0.1516 RANDOM 9.78
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] 0.38 -0.22 0.04 0.05 -0.12 -0.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.509 r_dihedral_angle_4_deg 19.801 r_dihedral_angle_3_deg 10.685 r_dihedral_angle_1_deg 6.268 r_sphericity_free 5.969 r_scangle_it 3.508 r_sphericity_bonded 3.197 r_scbond_it 2.659 r_mcangle_it 1.891 r_mcbond_it 1.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.509 r_dihedral_angle_4_deg 19.801 r_dihedral_angle_3_deg 10.685 r_dihedral_angle_1_deg 6.268 r_sphericity_free 5.969 r_scangle_it 3.508 r_sphericity_bonded 3.197 r_scbond_it 2.659 r_mcangle_it 1.891 r_mcbond_it 1.56 r_angle_refined_deg 1.484 r_rigid_bond_restr 1.307 r_angle_other_deg 0.941 r_mcbond_other 0.621 r_symmetry_vdw_other 0.323 r_nbd_refined 0.244 r_nbd_other 0.2 r_xyhbond_nbd_refined 0.18 r_nbtor_refined 0.179 r_symmetry_hbond_refined 0.17 r_symmetry_vdw_refined 0.141 r_nbtor_other 0.086 r_chiral_restr 0.082 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4297 Nucleic Acid Atoms Solvent Atoms 1354 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement SBC-Collect data collection HKL-3000 data reduction HKL-3000 data scaling HKL-3000 phasing