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Structure of UDP-galactopyranose mutase from Corynebacterium diphtheriae in complex with citrate ion
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BI7 PDB entry 2BI7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 298 100 mM sodium citrate, 15% isopropanol, 16-18% PEG5000 MME 2 VAPOR DIFFUSION, HANGING DROP 5.6 298 100 mM sodium citrate, 15% isopropanol, 16-18% PEG5000 MME. soaked in 100 mM potassium citrate, pH 5.6, 15% isopropanol, 18% PEG5000 MME prior to cryoprotection
Crystal Properties Matthews coefficient Solvent content 3.33 63.08 3.33 63.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.278 α = 90 b = 98.278 β = 90 c = 126.223 γ = 90
Symmetry Space Group P 41 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 MARMOSAIC 225 mm CCD 2014-10-12 M SINGLE WAVELENGTH 2 2 x-ray 100 CCD MARMOSAIC 325 mm CCD 2015-05-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F 2 SYNCHROTRON SSRL BEAMLINE BL14-1 1.181 SSRL BL14-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.95 50 99.9 0.103 0.105 0.02 8.7 23.6 45492 28.81
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2.02 99.6 0.756 0.775 0.164 0.923 20.1 4454
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 FREE R-VALUE PDB entry 2BI7 1.95 46.72 44055 2189 96.41 0.1546 0.1528 0.1544 0.1895 0.1889 32.7926
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 14.63 f_angle_d 1.047 f_chiral_restr 0.044 f_bond_d 0.008 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3165 Nucleic Acid Atoms Solvent Atoms 458 Heterogen Atoms 96
Software Software Software Name Purpose SCALEPACK data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction HKL-2000 data reduction