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Crystal structure of Dihyrodipicolinate Synthase (dapA)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1O5K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 Oil-batch 6.5 293 18% PEG 8000, 0.1M Cacodylate, 0.2M Ca Acetate, pH 6.5, Oil-batch, temperature 293.0K
Crystal Properties Matthews coefficient Solvent content 2.37 48.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.469 α = 90 b = 76.532 β = 106.87 c = 101.863 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 120 CCD MARMOSAIC 225 mm CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX10.1 0.979 SRS PX10.1
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 2.2 50 97.6 0.067 3.9 59985 58517 -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) 2.2 2.28 82.6 0.211 2.7 4918
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1O5K 2.2 20 55463 2965 97.47 0.16115 0.15774 0.22444 RANDOM 26.881
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] -1.97 -0.9 0.98 0.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.514 r_dihedral_angle_4_deg 19.352 r_dihedral_angle_3_deg 16.061 r_dihedral_angle_1_deg 6.852 r_scangle_it 5.369 r_scbond_it 3.374 r_angle_refined_deg 1.825 r_mcangle_it 1.721 r_mcbond_it 1.164 r_nbtor_refined 0.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.514 r_dihedral_angle_4_deg 19.352 r_dihedral_angle_3_deg 16.061 r_dihedral_angle_1_deg 6.852 r_scangle_it 5.369 r_scbond_it 3.374 r_angle_refined_deg 1.825 r_mcangle_it 1.721 r_mcbond_it 1.164 r_nbtor_refined 0.311 r_nbd_refined 0.246 r_symmetry_vdw_refined 0.229 r_xyhbond_nbd_refined 0.16 r_chiral_restr 0.129 r_symmetry_hbond_refined 0.128 r_bond_refined_d 0.022 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8849 Nucleic Acid Atoms Solvent Atoms 700 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MAR345dtb data collection HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing