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Crystal structure of human dermatan sulfate epimerase 1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other CRANK2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293.15 Ammonium acetate 200 mM,
MES 0.1 M (pH 6.5),
Glycerol ethoxylate 30% v/v,
Xylitol 6%
Crystal Properties Matthews coefficient Solvent content 5 75.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 182.676 α = 90 b = 213.914 β = 90 c = 86.945 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 PIXEL DECTRIS EIGER X 16M 2017-05-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.97967 MAX IV BioMAX
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.41 48.574 100 0.092 0.097 0.03 0.999 15.71 10.5 66029 1.03 67.29
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.41 2.446
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 CRANK2 2.41 48.574 1.34 66000 3272 99.98 0.1772 0.1756 0.1811 0.2089 0.2141
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 6.531 f_angle_d 0.775 f_chiral_restr 0.05 f_plane_restr 0.005 f_bond_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6009 Nucleic Acid Atoms Solvent Atoms 153 Heterogen Atoms 142
Software Software Software Name Purpose PHENIX refinement MxCuBE data collection XDS data reduction Aimless data scaling PHENIX model building PHASER phasing