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Succinate bound to pig GTP-specific succinyl-CoA synthetase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4XX0 PDB entry 4XX0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 294 PEG 3350, ammonium succinate, magnesium chloride, CoA, HEPES, pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.32 46.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.67 α = 90 b = 81.02 β = 104.9 c = 50.78 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 RAYONIX MX300HE 2014-09-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08B1-1 0.97947 CLSI 08B1-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 2.2 49.073 97 0.096 0.113 0.058 9.3 3.6 33544 33544 26.81
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.32 94.6 0.466 0.466 0.284 1.6 3.5 4750
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 PDB entry 4XX0 2.2 49.073 1.34 33535 3327 96.99 0.1695 0.1646 0.1671 0.2136 0.2142 30.7228
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 10.813 f_angle_d 0.542 f_chiral_restr 0.044 f_bond_d 0.003 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5205 Nucleic Acid Atoms Solvent Atoms 250 Heterogen Atoms 75
Software Software Software Name Purpose PHENIX refinement SCALA data scaling iMOSFLM data reduction Coot model building PHENIX phasing