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Crystal structure of human UDP-glucose dehydrogenase Thr131Ala, apo form.
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 6 293.15 15% PEG smears (PEG 400, 600, 1000, 2000, 3350, 4000, MME 5000, 6000, 8000, 10000), 0.1M MES pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K
Crystal Properties Matthews coefficient Solvent content 2.65 53.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.06 α = 90 b = 106.61 β = 90 c = 349.12 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 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 2.4 52.9 99.8 0.131 7.9 4 130411 2 40.1
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 2.4 2.53 99.4 0.55 2.1 3.3
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2Q3E 2.4 52.9 130411 128277 2134 99.7 0.199 0.198 0.1991 0.241 0.2421 RANDOM 12.77
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] -0.23 0.37 -0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.487 r_dihedral_angle_4_deg 17.501 r_dihedral_angle_3_deg 13.546 r_scangle_it 7.877 r_scbond_it 5.506 r_dihedral_angle_1_deg 5.449 r_mcangle_it 3.257 r_mcbond_it 1.793 r_angle_refined_deg 1.463 r_angle_other_deg 1.096
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.487 r_dihedral_angle_4_deg 17.501 r_dihedral_angle_3_deg 13.546 r_scangle_it 7.877 r_scbond_it 5.506 r_dihedral_angle_1_deg 5.449 r_mcangle_it 3.257 r_mcbond_it 1.793 r_angle_refined_deg 1.463 r_angle_other_deg 1.096 r_mcbond_other 0.618 r_chiral_restr 0.083 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_bond_other_d 0.003 r_gen_planes_other 0.003 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined 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 21621 Nucleic Acid Atoms Solvent Atoms 1188 Heterogen Atoms 133
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling