☰ Navigation Tabs
Crystal structure of an enolase (mandelate racemase subgroup) from paracococus denitrificans pd1222 (target nysgrc-012907) with bound mg
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PMQ pdb entry 2PMQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 298 Protein (10 mM Hepes, pH 7.8, 150 mM NaCl, 10% glycerol, 5 mM MgCl); Reservoir (0.1 M Magnesium Chloride 0.1 M MES:NaOH pH 6.5 30% (v/v) PEG 400); Cryoprotection (Reservoir), sitting drop vapor diffuction, temperature 298K, VAPOR DIFFUSION, SITTING DROP
Crystal Properties Matthews coefficient Solvent content 2.28 46.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.963 α = 90 b = 117.963 β = 90 c = 111.154 γ = 90
Symmetry Space Group P 4 21 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 2012-03-12 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 2 117.963 100 0.116 0.116 16.9 14.1 53519 53519
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 2 2.11 100 0.707 0.707 1.1 13.3 7688
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 (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 pdb entry 2PMQ 2 55.577 1.34 53463 53463 2713 99.93 0.1647 0.1647 0.1627 0.1652 0.202 0.2011 RANDOM 28.5934
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] -1.9847 -1.9847 3.9693
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.307 f_angle_d 1.083 f_chiral_restr 0.067 f_bond_d 0.008 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5413 Nucleic Acid Atoms Solvent Atoms 476 Heterogen Atoms 8
Software Software Software Name Purpose SCALA data scaling PHENIX refinement PDB_EXTRACT data extraction MOSFLM data reduction PHENIX phasing