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Crystal structure of an enolase from the soil bacterium Cellvibrio japonicus (TARGET EFI-502161) with bound MG and L-tartrate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QJM PDB ENTRY 2QJM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 sitting drop vapor diffusion 4.6 298 Protein (10 mM Hepes, pH 7.8, 150 mM NaCl, 10% glycerol, 5 mM DTT, 5 mM MgCl2; Reservoir (0.2M KNaTartrate, 20% Peg3350); Cryoprotection (20% glycerol), sitting drop vapor diffusion, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.24 45.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 124.715 α = 90 b = 124.715 β = 90 c = 110.871 γ = 90
Symmetry Space Group I 4 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 RAYONIX MX225HE MIRRORS 2011-11-15 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 1.4 88.187 100 0.071 0.071 25.2 13.9 85453 85453 10.8
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 1.4 1.48 100 0.623 0.623 1.3 12.6 12354
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB ENTRY 2QJM 1.4 32.136 1.34 85437 85437 4276 99.99 0.1493 0.1486 0.1464 0.1618 0.1594 Random 15.0059
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] 0.4182 0.4182 -0.8363
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.821 f_angle_d 1.628 f_chiral_restr 0.11 f_bond_d 0.017 f_plane_restr 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3076 Nucleic Acid Atoms Solvent Atoms 475 Heterogen Atoms 12
Software Software Software Name Purpose SCALA data scaling PHENIX refinement PDB_EXTRACT data extraction MAR345dtb data collection MOSFLM data reduction PHENIX phasing