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Triphosphate tunnel metalloenzyme from Sulfolobus acidocaldarius in complex with pyrophosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7NS9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 Crystals were grown in 1:1 mixtures of JCSG Core IA11 (0.2M Potassium acetate, 20%(w/v) PEG 3350) and 10 mg/ml protein in 200 mM NaCl, 50 mM Tris, pH 9.0
Crystal Properties Matthews coefficient Solvent content 3.05 59.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.312 α = 90 b = 61.312 β = 90 c = 138.535 γ = 90
Symmetry Space Group P 41 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 PIXEL DECTRIS PILATUS 6M 2018-12-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.972 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) 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 2.7 45.91 78.54 0.03404 0.04814 0.999 8.7 1.9 6390 58.47
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.8 0.778
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 7NS9 2.7 45.91 1.33 6124 289 78.59 0.291 0.2895 0.282 0.3184 0.3137 61.29
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 16.2995 f_angle_d 1.4997 f_chiral_restr 0.1037 f_bond_d 0.0119 f_plane_restr 0.0086
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1447 Nucleic Acid Atoms Solvent Atoms 30 Heterogen Atoms 10
Software Software Software Name Purpose PHENIX refinement Aimless data scaling PHASER phasing XDS data reduction