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The Crystal Structure of Dihydrodipicolinate Synthase DapA from Agrobacterium tumefaciens
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 295 0.2M Tri-Lithium Citrate, 20% PEG3350, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.37 48.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.102 α = 90 b = 101.102 β = 90 c = 120.914 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 SBC-3 mirrors 2006-06-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.97910 APS 19-BM
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 1.9 31.92 99.8 0.104 6.1 25.6 29275 29211
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 1.9 1.93 99.6 0.555 3.5 18.6 1404
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 1.9 31.92 25301 25301 2813 96.06 0.19315 0.19315 0.18715 0.1862 0.24674 0.2448 RANDOM 32.017
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] 1.67 0.83 1.67 -2.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.235 r_dihedral_angle_4_deg 18.209 r_dihedral_angle_3_deg 14.975 r_dihedral_angle_1_deg 5.815 r_scangle_it 3.549 r_scbond_it 2.305 r_angle_refined_deg 1.415 r_mcangle_it 1.252 r_mcbond_it 0.899 r_nbtor_refined 0.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.235 r_dihedral_angle_4_deg 18.209 r_dihedral_angle_3_deg 14.975 r_dihedral_angle_1_deg 5.815 r_scangle_it 3.549 r_scbond_it 2.305 r_angle_refined_deg 1.415 r_mcangle_it 1.252 r_mcbond_it 0.899 r_nbtor_refined 0.311 r_nbd_refined 0.214 r_symmetry_vdw_refined 0.194 r_xyhbond_nbd_refined 0.17 r_symmetry_hbond_refined 0.149 r_chiral_restr 0.099 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2388 Nucleic Acid Atoms Solvent Atoms 409 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling HKL-3000 phasing SHELXE model building SOLVE phasing RESOLVE phasing ARP/wARP model building