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Crystal Structure of C-terminal truncation of UDP-glucose Pyrophosphorylase of Homo sapiens
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3R2W PDB ENTRY 3R2W
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 290 magnesium sulfate, PEG3350, glycerol, HEPES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 3.78 67.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 140.266 α = 90 b = 140.266 β = 90 c = 315.284 γ = 120
Symmetry Space Group P 31 2 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 2010-10-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U SSRF BL17U
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 3.566 19.981 97.9 0.095 7.9 43409 42839 1 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 3.566 3.61 61.2 0.649
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 THROUGHOUT PDB ENTRY 3R2W 3.57 19.98 42839 2162 98.69 0.2353 0.2326 0.2286 0.2862 0.2857 RANDOM 175.894
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] -0.66 -0.33 -0.66 1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.667 r_dihedral_angle_3_deg 21.115 r_dihedral_angle_4_deg 19.658 r_dihedral_angle_1_deg 6.477 r_scangle_it 2.049 r_angle_refined_deg 1.559 r_scbond_it 1.15 r_mcangle_it 0.938 r_mcbond_it 0.491 r_chiral_restr 0.102
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.667 r_dihedral_angle_3_deg 21.115 r_dihedral_angle_4_deg 19.658 r_dihedral_angle_1_deg 6.477 r_scangle_it 2.049 r_angle_refined_deg 1.559 r_scbond_it 1.15 r_mcangle_it 0.938 r_mcbond_it 0.491 r_chiral_restr 0.102 r_bond_refined_d 0.013 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13580 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction PHASER phasing