☰ Navigation Tabs
Crystal structure of T. acidophilum isopentenyl phosphate kinase product complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other T. acidophilum isopentenyl phosphate kinase solved by single wavelength anomalous diffraction
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 274 0.1 M PCB buffer (2:1:2 molar ratio of sodium propionate, sodium cacodylate, Bis-Tris propane, pH 6.0 containing 25% PEG1500, VAPOR DIFFUSION, SITTING DROP, temperature 274K
Crystal Properties Matthews coefficient Solvent content 2.21 44.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 187.104 α = 90 b = 42.787 β = 113.19 c = 134.895 γ = 90
Symmetry Space Group C 1 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 MARMOSAIC 325 mm CCD Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing) 2009-02-27 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.97887 SSRL BL11-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.99 50 0.062 9.48 1.8 65826
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.99 2.06 0.062 3.3 1.7
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT T. acidophilum isopentenyl phosphate kinase solved by single wavelength anomalous diffraction 1.987 38.292 1.34 69169 65826 3342 95.96 0.1954 0.193 0.1949 0.2384 0.2391
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] 0.5158 -3.4756 -1.3365 0.8207
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 17.754 f_angle_d 1.975 f_chiral_restr 0.115 f_bond_d 0.021 f_plane_restr 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7261 Nucleic Acid Atoms Solvent Atoms 240 Heterogen Atoms 164
Software Software Software Name Purpose CrystalClear data collection PHASER phasing PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling