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Crystal structure of human UDP-glucose dehydrogenase product complex with UDP-glucuronate
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 6.5 277 20% PEG 3350, 10% Ethylene glycol, 0.2 M NaBr, 0.1 M Bis-tris-propane, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.06 59.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 193.868 α = 90 b = 193.868 β = 90 c = 352.223 γ = 120
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 2007-04-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.033 SLS X10SA
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 2.1 60 100 0.139 7.6 3.9 288088 288088 17
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 2.1 2.21 100 1.8 3.8 42048
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 2Q3E 2.1 59.66 273217 273217 14846 100 0.17832 0.17832 0.17574 0.1781 0.22496 0.2248 THIN SHELLS 13.44
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] -0.15 -0.08 -0.15 0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.586 r_dihedral_angle_4_deg 16.87 r_dihedral_angle_3_deg 12.491 r_scangle_it 5.926 r_dihedral_angle_1_deg 5.576 r_scbond_it 4.394 r_mcangle_it 2.559 r_mcbond_it 1.737 r_angle_refined_deg 1.238 r_angle_other_deg 0.909
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.586 r_dihedral_angle_4_deg 16.87 r_dihedral_angle_3_deg 12.491 r_scangle_it 5.926 r_dihedral_angle_1_deg 5.576 r_scbond_it 4.394 r_mcangle_it 2.559 r_mcbond_it 1.737 r_angle_refined_deg 1.238 r_angle_other_deg 0.909 r_mcbond_other 0.505 r_symmetry_vdw_other 0.235 r_nbd_refined 0.191 r_nbd_other 0.185 r_nbtor_refined 0.17 r_xyhbond_nbd_refined 0.143 r_symmetry_hbond_refined 0.134 r_symmetry_vdw_refined 0.114 r_nbtor_other 0.083 r_chiral_restr 0.072 r_symmetry_hbond_other 0.012 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 28503 Nucleic Acid Atoms Solvent Atoms 2999 Heterogen Atoms 604
Software Software Software Name Purpose REFMAC refinement MAR345 data collection MOSFLM data reduction SCALA data scaling PHASER phasing