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Crystal structure of putative ribokinase (10640157) from Thermoplasma acidophilum at 1.91 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.5 277 NANODROP, 40.0% 1,2-propanediol, 0.1M Acetate pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.08 40.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.45 α = 90 b = 59.18 β = 90 c = 177.65 γ = 90
Symmetry Space Group P 21 21 21
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 300 mm CCD Adjustable focusing mirrors in K-B geometry 2007-10-26 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 0.91840, 0.97939, 0.97953 APS 23-ID-D
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 1.91 29.185 98.4 0.05 10.78 46740 -3 36.803
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 1.91 1.98 99.6 0.685 1.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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 MAD THROUGHOUT 1.91 29.185 46708 2364 99.12 0.205 0.202 0.2062 0.245 0.2474 RANDOM 34.325
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] 2.39 0.3 -2.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.909 r_dihedral_angle_4_deg 14.311 r_dihedral_angle_3_deg 12.183 r_scangle_it 5.879 r_scbond_it 4.387 r_dihedral_angle_1_deg 3.758 r_mcangle_it 2.42 r_mcbond_it 1.636 r_angle_refined_deg 1.596 r_angle_other_deg 1.272
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.909 r_dihedral_angle_4_deg 14.311 r_dihedral_angle_3_deg 12.183 r_scangle_it 5.879 r_scbond_it 4.387 r_dihedral_angle_1_deg 3.758 r_mcangle_it 2.42 r_mcbond_it 1.636 r_angle_refined_deg 1.596 r_angle_other_deg 1.272 r_mcbond_other 0.45 r_nbd_refined 0.167 r_nbtor_refined 0.158 r_symmetry_vdw_other 0.156 r_nbd_other 0.136 r_symmetry_hbond_refined 0.113 r_xyhbond_nbd_refined 0.098 r_chiral_restr 0.086 r_symmetry_vdw_refined 0.081 r_nbtor_other 0.072 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4352 Nucleic Acid Atoms Solvent Atoms 214 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SOLVE phasing MolProbity model building XSCALE data scaling PDB_EXTRACT data extraction MAR345 data collection XDS data reduction