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Sulfolobus solfataricus ribose-phosphate pyrophosphokinase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1U9Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 5 293 Protein:
12.7 mg/mL
50 mM Tris/HCl pH 7.6
10 mM AMP
10 mM ribose 5-phosphate
Buffer:
0.2 M diammonium citrate pH 5.0
Precipitant:
14 % PEG10000
Crystal Properties Matthews coefficient Solvent content 2.66 53.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.217 α = 90 b = 92.846 β = 90.91 c = 138.338 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 120 CCD MARRESEARCH 2010-01-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I911-2 1.03908 MAX II I911-2
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 2.8 20 97.9 0.089 14 4.1 48432 48432
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 2.8 2.9 98.1 0.59 2.4 4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 FREE R-VALUE 1U9Y 2.802 19.984 1.33 48382 2406 97.9 0.2361 0.2346 0.2321 0.2647 0.2331 5 % random selection
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] 6.7424 -16.2902 -0.312 -6.4304
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 18.755 f_angle_d 1.306 f_chiral_restr 0.082 f_bond_d 0.009 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13002 Nucleic Acid Atoms Solvent Atoms 24 Heterogen Atoms 168
Software Software Software Name Purpose SCALEPACK data scaling PHENIX refinement