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The crystal structure of the nucleoside-diphosphate-sugar epimerase from Agrobacterium tumefaciens
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 298 0.1M Tris, 3.5M Na Formate, 0.1M MES6.0, 20% PEG10K, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.58 52.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.893 α = 90 b = 112.893 β = 90 c = 52.765 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 ADSC QUANTUM 315 mirrors 2006-04-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.9798 APS 19-ID
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 1.85 97.59 99.59 0.084 32.98 13.6 31621 31491 2 2 28
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 1.85 1.9 99.75 0.69 2.53 12.1 2313
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 (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 SAD THROUGHOUT 1.85 37 31621 31491 1677 99.59 0.18647 0.18647 0.18455 0.1832 0.22457 0.2233 RANDOM 28.539
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] 0.52 0.26 0.52 -0.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.357 r_dihedral_angle_4_deg 19.017 r_dihedral_angle_3_deg 13.624 r_dihedral_angle_1_deg 6.088 r_scangle_it 3.663 r_scbond_it 2.319 r_angle_refined_deg 1.243 r_mcangle_it 1.225 r_mcbond_it 0.862 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.357 r_dihedral_angle_4_deg 19.017 r_dihedral_angle_3_deg 13.624 r_dihedral_angle_1_deg 6.088 r_scangle_it 3.663 r_scbond_it 2.319 r_angle_refined_deg 1.243 r_mcangle_it 1.225 r_mcbond_it 0.862 r_nbtor_refined 0.305 r_symmetry_hbond_refined 0.2 r_nbd_refined 0.197 r_symmetry_vdw_refined 0.196 r_xyhbond_nbd_refined 0.163 r_chiral_restr 0.087 r_bond_refined_d 0.012 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2621 Nucleic Acid Atoms Solvent Atoms 316 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling HKL-3000 phasing SHELXE model building SOLVE phasing RESOLVE phasing ARP/wARP model building