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Role of Packing Defects in the Evolution of Allostery and Induced Fit in Human UDP-Glucose Dehydrogenase.
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, HANGING DROP 7.5 298 10% PEG3350, 6% heptanediol, 0.1 M HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.75 55.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.1 α = 90 b = 196.67 β = 111.88 c = 111.744 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 MAR 300 2009-01-01 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1 APS 22-ID
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 2.5 49.167 97.5 0.071 15.7 3.8 122905 119611
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.63 91.5 0.39 0.39 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 2.5 49.167 119611 113593 6018 97.32 0.19237 0.18889 0.1898 0.25778 0.2557 RANDOM 31.542
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] 0.02 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.904 r_dihedral_angle_4_deg 21.796 r_dihedral_angle_3_deg 17.547 r_dihedral_angle_1_deg 6.409 r_scangle_it 4.05 r_scbond_it 2.47 r_angle_refined_deg 1.797 r_mcangle_it 1.431 r_mcbond_it 0.742 r_chiral_restr 0.063
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.904 r_dihedral_angle_4_deg 21.796 r_dihedral_angle_3_deg 17.547 r_dihedral_angle_1_deg 6.409 r_scangle_it 4.05 r_scbond_it 2.47 r_angle_refined_deg 1.797 r_mcangle_it 1.431 r_mcbond_it 0.742 r_chiral_restr 0.063 r_bond_refined_d 0.018 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 21502 Nucleic Acid Atoms Solvent Atoms 783 Heterogen Atoms 468
Software Software Software Name Purpose SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction MAR345 data collection XDS data reduction