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Crystal structure of EFI-502318, an enolase family member from Agrobacterium tumefaciens with homology to dipeptide epimerases (bound sodium, L-Ala-L-Glu with ordered loop)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JPD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 298 Protein (10 mM Tris pH 7.5, 5 mM MgCl, 50 mM L-Ala,L-Glu), Reservoir (0.1 M HEPES:NaOH pH 7.5, 2.0 M Ammonium Sulfate), Cryoprotection (Drop was superconcentrated, no added cryoprotection required), sitting drop vapor diffusion, temperature 298K, VAPOR DIFFUSION, SITTING DROP
Crystal Properties Matthews coefficient Solvent content 2.27 45.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.901 α = 90 b = 77.274 β = 90 c = 215.825 γ = 90
Symmetry Space Group P 21 21 21
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 RAYONIX MX225HE MIRRORS 2012-07-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.9793 APS 31-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.9 107.912 100 0.085 0.085 17.2 7.4 102243 102243
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.92 100 0.737 0.737 2.8 7.4
Refinement Statistics Diffraction ID Structure Solution 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 1JPD 1.9 62.827 102114 102114 5097 99.95 0.1731 0.1731 0.171 0.1729 0.2134 0.2123 RANDOM 22.6225
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.638 f_angle_d 1.087 f_chiral_restr 0.071 f_bond_d 0.008 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9789 Nucleic Acid Atoms Solvent Atoms 701 Heterogen Atoms 95
Software Software Software Name Purpose SCALA data scaling PHENIX refinement PDB_EXTRACT data extraction MOSFLM data reduction PHENIX phasing