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Structure of human UDP-glucose dehydrogenase complexed with NADH and UDP-glucose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2O3J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 277 16% PEG 3350, 8% EG, 160 mM NaBr, 80 mM BTP., pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.76 55.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.99 α = 90 b = 184.132 β = 109.23 c = 170.943 γ = 90
Symmetry Space Group P 1 21 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 MARMOSAIC 225 mm CCD 2007-05-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.9999 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 50 99.6 0.089 9.7 3.9 452865 452865 28
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 2.11 99.1 0.636 2 3.9 65636
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 2o3j 2 49.09 429343 429343 23473 100 0.17343 0.17343 0.17163 0.1763 0.20521 0.2092 THIN SHELLS 26.333
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] 1.82 2.37 -1.26 1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.976 r_dihedral_angle_4_deg 17.948 r_dihedral_angle_3_deg 12.539 r_scangle_it 5.266 r_dihedral_angle_1_deg 5.244 r_scbond_it 3.894 r_mcangle_it 2.275 r_mcbond_it 1.647 r_angle_refined_deg 1.234 r_angle_other_deg 0.943
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.976 r_dihedral_angle_4_deg 17.948 r_dihedral_angle_3_deg 12.539 r_scangle_it 5.266 r_dihedral_angle_1_deg 5.244 r_scbond_it 3.894 r_mcangle_it 2.275 r_mcbond_it 1.647 r_angle_refined_deg 1.234 r_angle_other_deg 0.943 r_mcbond_other 0.57 r_symmetry_vdw_other 0.266 r_nbd_refined 0.194 r_nbd_other 0.185 r_symmetry_hbond_refined 0.181 r_nbtor_refined 0.172 r_xyhbond_nbd_refined 0.128 r_symmetry_vdw_refined 0.09 r_nbtor_other 0.082 r_chiral_restr 0.078 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_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 42755 Nucleic Acid Atoms Solvent Atoms 2745 Heterogen Atoms 972
Software Software Software Name Purpose REFMAC refinement MAR345 data collection MOSFLM data reduction SCALA data scaling PHASER phasing