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Crystal structure of an enolase family member from vibrio harveyi (efi-target 501692) with homology to mannonate dehydratase, with mg, hepes, and ethylene glycol bound (ordered loops, space group c2221)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3R25
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 298 Protein (10 mM Hepes, 150 mM NaCl, 10% glycerol, 1 mM DTT, 5 mM MgCl); Reservoir (200 mM NaCl, 0.1 M Hepes, 25% Peg3350); Cryoprotection (Reservoir, + 20% ethylene glycol and 50 mM MgCl), pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.63 53.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.948 α = 90 b = 209.55 β = 90 c = 208.468 γ = 90
Symmetry Space Group C 2 2 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 2011-07-27 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 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 1.9 104.775 99.2 0.113 11.1 5 158060 158060
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 2 98.4 0.592 0.592 1.1 4.4 22659
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 3R25 1.9 93.616 157249 157249 4735 98.63 0.1694 0.1694 0.1683 0.1726 0.2034 0.2071 RANDOM 18.3586
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 14.47 f_angle_d 1.096 f_chiral_restr 0.077 f_bond_d 0.008 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12760 Nucleic Acid Atoms Solvent Atoms 1694 Heterogen Atoms 141
Software Software Software Name Purpose SCALA data scaling PHENIX refinement PDB_EXTRACT data extraction MOSFLM data reduction PHENIX phasing