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Crystal structure of human UDP-glucose dehydrogenase Glu161Gln, in complex with thiohemiacetal intermediate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Q3E PDB entry 2Q3E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277.15 18% PEG smears (PEG 400, 600, 1000, 2000, 3350, 4000, 5000 MME, 6000, 8000, 10000), 0.1M HEPES pH 7.5, 5% Ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K
Crystal Properties Matthews coefficient Solvent content 3.15 60.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 203.54 α = 90 b = 207.34 β = 90 c = 93.4 γ = 90
Symmetry Space Group P 21 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 ADSC QUANTUM 315 mirrors 2009-07-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.3 48.74 99.8 0.106 9.4 4.3 175207 175139 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.42 100 0.743 2 4.3 25412
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 2Q3E 2.3 48.74 175128 173128 1988 99.71 0.19544 0.19509 0.2252 0.2383 RANDOM 19.743
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] -3.2 0.75 2.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.178 r_dihedral_angle_4_deg 20.67 r_dihedral_angle_3_deg 13.744 r_scangle_it 7.651 r_scbond_it 5.293 r_dihedral_angle_1_deg 5.28 r_mcangle_it 2.975 r_mcbond_it 1.593 r_angle_refined_deg 1.438 r_angle_other_deg 1.007
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.178 r_dihedral_angle_4_deg 20.67 r_dihedral_angle_3_deg 13.744 r_scangle_it 7.651 r_scbond_it 5.293 r_dihedral_angle_1_deg 5.28 r_mcangle_it 2.975 r_mcbond_it 1.593 r_angle_refined_deg 1.438 r_angle_other_deg 1.007 r_mcbond_other 0.326 r_chiral_restr 0.095 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 21667 Nucleic Acid Atoms Solvent Atoms 1314 Heterogen Atoms 515
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling