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Crystal structure of Thermus thermophilus HB8 UDP-glucose 4-epimerase complex with NAD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2P5U PDB entry 2P5U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 293 USING 1 MICROLITER DROPS CONTAINING EQUAL VOLUMES OF PROTEIN CONCENTRATE (11.71 mg/ml) AND RESERVOIR SOLUTION CONTAINING 1.0M Magnesium sulfate, 0.1M Sodium citrate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.07 60
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 135.667 α = 90 b = 135.667 β = 90 c = 135.667 γ = 90
Symmetry Space Group P 41 3 2
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 MARMOSAIC 225 mm CCD mirrors 2007-03-01 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 0.97928 APS 22-BM
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 1.92 50 100 0.068 15.2 42.4 33164 33164
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) 1.92 1.99 100 0.312 41.4 3230
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 2P5U 1.92 30 33064 33064 1673 99.95 0.192 0.191 0.1908 0.207 0.2071 RANDOM 25.125
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.207 r_dihedral_angle_4_deg 15.544 r_dihedral_angle_3_deg 13.564 r_dihedral_angle_1_deg 5.335 r_scangle_it 3.557 r_scbond_it 2.193 r_mcangle_it 1.343 r_angle_refined_deg 1.282 r_mcbond_it 0.89 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.207 r_dihedral_angle_4_deg 15.544 r_dihedral_angle_3_deg 13.564 r_dihedral_angle_1_deg 5.335 r_scangle_it 3.557 r_scbond_it 2.193 r_mcangle_it 1.343 r_angle_refined_deg 1.282 r_mcbond_it 0.89 r_nbtor_refined 0.306 r_nbd_refined 0.188 r_symmetry_vdw_refined 0.168 r_xyhbond_nbd_refined 0.141 r_symmetry_hbond_refined 0.112 r_chiral_restr 0.085 r_bond_refined_d 0.011 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2387 Nucleic Acid Atoms Solvent Atoms 217 Heterogen Atoms 44
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction SERGUI data collection HKL-2000 data reduction EPMR phasing