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Crystal structure of UDP-glucose 6-dehydrogenase from Porphyromonas gingivalis bound to product UDP-glucuronate
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 5.4 294 100mM Bis-Tris pH 5.4, 21% PEG 3350, 50mM magnesium chloride, vapor diffusion, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.34 47.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.365 α = 90 b = 143.489 β = 112.46 c = 85.501 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 CCD 165 mm 2009-01-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.97958 APS 31-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.7 44.368 93.7 0.117 0.117 8.1 4.7 200814 188163 19.2
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) 1.7 1.79 96.1 0.412 0.412 2.9 4.9 28175
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 1.7 20 200708 188003 9488 93.67 0.217 0.215 0.2193 0.256 0.2598 RANDOM 27.97
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] -0.48 -0.49 0.36 -0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.038 r_dihedral_angle_4_deg 16.973 r_dihedral_angle_3_deg 14.039 r_dihedral_angle_1_deg 5.658 r_scangle_it 3.777 r_scbond_it 2.482 r_angle_refined_deg 1.531 r_mcangle_it 1.36 r_mcbond_it 0.787 r_chiral_restr 0.101
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.038 r_dihedral_angle_4_deg 16.973 r_dihedral_angle_3_deg 14.039 r_dihedral_angle_1_deg 5.658 r_scangle_it 3.777 r_scbond_it 2.482 r_angle_refined_deg 1.531 r_mcangle_it 1.36 r_mcbond_it 0.787 r_chiral_restr 0.101 r_bond_refined_d 0.015 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13150 Nucleic Acid Atoms Solvent Atoms 1307 Heterogen Atoms 222
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction MAR345 data collection MOSFLM data reduction SHELXCD phasing SHELXE model building