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Crystal structure of a putative ribokinase from Agrobacterium tumefaciens
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 292 0.1M Bis-Tris pH 6.5, 1.5M Ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 3.07 59.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.024 α = 90 b = 81.024 β = 90 c = 139.799 γ = 90
Symmetry Space Group P 43 21 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 CUSTOM-MADE 2006-04-20 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.97873, 0.97886 APS 19-BM
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 1.9 50 99.8 0.059 9.9 7 69844 69844 -3 30.6
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 1.9 1.94 98.4 0.235 6.3 4.4 4637
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 MAD THROUGHOUT 1.9 32.17 35713 35713 1802 95.51 0.19 0.19 0.188 0.1916 0.228 0.2242 RANDOM 20.905
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] 0.83 0.83 -1.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.518 r_dihedral_angle_4_deg 13.459 r_dihedral_angle_3_deg 12.603 r_dihedral_angle_1_deg 6.106 r_scangle_it 3.575 r_scbond_it 2.678 r_angle_refined_deg 1.49 r_mcangle_it 1.327 r_mcbond_it 1.304 r_angle_other_deg 0.944
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.518 r_dihedral_angle_4_deg 13.459 r_dihedral_angle_3_deg 12.603 r_dihedral_angle_1_deg 6.106 r_scangle_it 3.575 r_scbond_it 2.678 r_angle_refined_deg 1.49 r_mcangle_it 1.327 r_mcbond_it 1.304 r_angle_other_deg 0.944 r_mcbond_other 0.231 r_nbd_refined 0.21 r_nbd_other 0.201 r_symmetry_vdw_other 0.193 r_xyhbond_nbd_refined 0.189 r_nbtor_refined 0.175 r_symmetry_vdw_refined 0.148 r_symmetry_hbond_refined 0.127 r_chiral_restr 0.089 r_nbtor_other 0.088 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2295 Nucleic Acid Atoms Solvent Atoms 400 Heterogen Atoms 52
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MLPHARE phasing DM phasing REFMAC refinement PDB_EXTRACT data extraction SBC-Collect data collection HKL-3000 data reduction HKL-3000 data scaling HKL-3000 phasing SHELXD phasing SHELXE model building SOLVE phasing RESOLVE phasing ARP/wARP model building CCP4 phasing O model building Coot model building