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Crystal structure of Dihydrodipicolinate synthase from Acinetobacter baumannii complexed with Mg and Cl ions at 1.80 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3RK8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.2 298 0.2M MgCl2, PEG 3350, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.37 48.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.35 α = 90 b = 122.47 β = 115.92 c = 52.33 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 77 CCD MARRESEARCH mirror 2011-10-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.97 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.8 61.24 99.3 0.103 14.4 50787 50787
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.83 98 0.56 2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT 3RK8 1.8 61.24 50787 50787 2720 99.55 0.15454 0.15454 0.15217 0.1524 0.19875 0.1968 RANDOM 17.073
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 0.08 -0.64 -0.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.097 r_dihedral_angle_4_deg 15.555 r_dihedral_angle_3_deg 14.67 r_dihedral_angle_1_deg 6.221 r_scangle_it 6.054 r_scbond_it 3.801 r_angle_refined_deg 2.121 r_mcangle_it 2.048 r_mcbond_it 1.25 r_chiral_restr 0.164
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.097 r_dihedral_angle_4_deg 15.555 r_dihedral_angle_3_deg 14.67 r_dihedral_angle_1_deg 6.221 r_scangle_it 6.054 r_scbond_it 3.801 r_angle_refined_deg 2.121 r_mcangle_it 2.048 r_mcbond_it 1.25 r_chiral_restr 0.164 r_bond_refined_d 0.027 r_gen_planes_refined 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4390 Nucleic Acid Atoms Solvent Atoms 637 Heterogen Atoms 9
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing REFMAC refinement DENZO data reduction SCALA data scaling