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Structure of UDP-galactopyranose mutase bound to UDP-glucose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BI8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 298 5 mg/mL protein, 85 mM ammonium acetate, 42 mM tri-sodium citrate, 12.3% PEG 4000, 7.5% glycerol, 15 mM L-cysteine, 5 mM UDP-Glc, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.18 61.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.951 α = 90 b = 93.951 β = 90 c = 130.259 γ = 90
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 rhodium coated toroidal mirror 2006-10-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-ID-B 0.9002 APS 14-ID-B
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 2.45 50 98.6 0.11 14.831 4.9 41757 41161 53.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.45 2.54 97 0.366 4.2 4.9 4042
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 2BI8 2.45 30 41510 40988 2064 98.74 0.194 0.194 0.192 0.1872 0.238 0.2297 RANDOM 45.792
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] -1.79 -1.79 3.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.225 r_dihedral_angle_4_deg 19.512 r_dihedral_angle_3_deg 16.612 r_dihedral_angle_1_deg 6.663 r_scangle_it 3.974 r_scbond_it 2.857 r_angle_refined_deg 1.712 r_mcangle_it 1.698 r_mcbond_it 1.466 r_nbtor_refined 0.322
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.225 r_dihedral_angle_4_deg 19.512 r_dihedral_angle_3_deg 16.612 r_dihedral_angle_1_deg 6.663 r_scangle_it 3.974 r_scbond_it 2.857 r_angle_refined_deg 1.712 r_mcangle_it 1.698 r_mcbond_it 1.466 r_nbtor_refined 0.322 r_nbd_refined 0.225 r_symmetry_vdw_refined 0.18 r_symmetry_hbond_refined 0.179 r_xyhbond_nbd_refined 0.158 r_chiral_restr 0.117 r_bond_refined_d 0.018 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6238 Nucleic Acid Atoms Solvent Atoms 195 Heterogen Atoms 163
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