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Crystal Structure of Human UDP-Glucose Dehydrogenase
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 vapr diffusion 6.5 298 0.2M Ammonium sulfate, 21% PEG 8000, 0.1M Sodium cacodylate, pH 6.5, vapr diffusion, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.87 57.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 173.132 α = 90 b = 191.177 β = 90 c = 225.807 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray AREA DETECTOR 2005-07-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 4A 1.00 PAL/PLS 4A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.8 145.91 96.1 0.127 8 4.9 176566 176566
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.95 90.5 0.517 0.517 0.599 0.292 1.4 3.7 24023
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.8 145.91 176232 8844 95.77 0.2314 0.2298 0.2286 0.2609 0.2562 RANDOM 50.952
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] 0.27 -2.59 2.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.086 r_dihedral_angle_4_deg 18.841 r_dihedral_angle_3_deg 17.478 r_dihedral_angle_1_deg 5.337 r_scangle_it 2.489 r_scbond_it 1.471 r_angle_refined_deg 1.462 r_mcangle_it 0.904 r_mcbond_it 0.48 r_chiral_restr 0.094
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.086 r_dihedral_angle_4_deg 18.841 r_dihedral_angle_3_deg 17.478 r_dihedral_angle_1_deg 5.337 r_scangle_it 2.489 r_scbond_it 1.471 r_angle_refined_deg 1.462 r_mcangle_it 0.904 r_mcbond_it 0.48 r_chiral_restr 0.094 r_bond_refined_d 0.014 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 43236 Nucleic Acid Atoms Solvent Atoms 579 Heterogen Atoms 852
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction ADSC data collection