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Crystal structure of human UDP-xylose synthase.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2B69 PDB ENTRY 2B69
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 298 1.3 M AMMONIUM SULFATE, 0.1 M MAGNESIUM FORMATE AND 0.15% 1.5K PEG, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.96 58.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 125.61 α = 90 b = 125.61 β = 90 c = 98.92 γ = 120
Symmetry Space Group P 32 2 1
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 ADSC QUANTUM 210 2007-01-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.1 1.0 ALS 8.2.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.5 50 97.3 31483 31483
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 2.5 2.57 90
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation 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 THROUGHOUT PDB ENTRY 2B69 2.5 45 29894 29894 1589 99.8 0.209 0.18 0.178 0.1767 0.223 0.2214 RANDOM 39.67
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] 0.02 0.01 0.02 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.542 r_dihedral_angle_4_deg 20.079 r_dihedral_angle_3_deg 19.217 r_dihedral_angle_1_deg 7.899 r_scangle_it 5.189 r_mcangle_it 4.581 r_scbond_it 3.423 r_mcbond_it 2.911 r_angle_refined_deg 1.44 r_chiral_restr 0.112
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.542 r_dihedral_angle_4_deg 20.079 r_dihedral_angle_3_deg 19.217 r_dihedral_angle_1_deg 7.899 r_scangle_it 5.189 r_mcangle_it 4.581 r_scbond_it 3.423 r_mcbond_it 2.911 r_angle_refined_deg 1.44 r_chiral_restr 0.112 r_bond_refined_d 0.014 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4837 Nucleic Acid Atoms Solvent Atoms 136 Heterogen Atoms 106
Software Software Software Name Purpose REFMAC refinement CNS refinement XDS data reduction XDS data scaling CNS phasing