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The crystal structure of D-ribulose 5-phosphate 3-epimerase from Streptococus pyogenes complexed with D-xylitol 5-phosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TQJ PDB ENTRY 1TQJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 19% PEG 3350, 0.1M Succinic acid, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal Properties Matthews coefficient Solvent content 2.31 46.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.022 α = 90 b = 199.449 β = 109.76 c = 87.622 γ = 90
Symmetry Space Group P 1 21 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 4 2005-10-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X4A 0.979 NSLS X4A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.8 24.99 94.9 229414 229414 14.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.8 1.86 88.7
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1TQJ 1.8 24.99 229414 229414 10427 0.227 0.227 0.224 0.256 RANDOM 27.3
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] 4.24 4.02 -5.51 1.27
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.8 c_scangle_it 2.81 c_scbond_it 1.98 c_mcangle_it 1.79 c_mcbond_it 1.23 c_angle_deg 1.2 c_improper_angle_d 0.77 c_bond_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 19738 Nucleic Acid Atoms Solvent Atoms 968 Heterogen Atoms 180
Software Software Software Name Purpose CNS refinement DENZO data reduction SCALEPACK data scaling EPMR phasing