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Crystal structure of a succinyl-diaminopimelate desuccinylase (ArgE) from Corynebacterium glutamicum ATCC 13032 at 2.97 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VGY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.41 293 43.1% polyethylene glycol 400, 0.20M sodium chloride, 0.1M Na/K phosphate pH 6.41, Additive: 0.006 M zinc chloride, nanodrop, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 4.47 72.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.901 α = 90 b = 82.901 β = 90 c = 364.175 γ = 120
Symmetry Space Group P 65 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 MARMOSAIC 325 mm CCD double crystal monochromator 2010-05-13 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.91162,0.97919,0.97936 SSRL BL9-2
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 2.97 29.543 99.1 0.095 13.1 4.6 16179 -3 91.327
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 2.97 3.05 98.5 1.248 1.5 4.8
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT + MAD 1VGY 2.972 29.543 1.87 16098 1649 99.07 0.2399 0.2379 0.2404 0.2566 0.2521 99.6661
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] 18.0032 18.0032 -36.0064
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 11.38 f_angle_d 0.625 f_chiral_restr 0.047 f_bond_d 0.003 f_plane_restr 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2744 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 6
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction XSCALE data scaling PHASER phasing CNS phasing CNS refinement MolProbity model building XDS data reduction