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Thermus aquaticus succinyl-CoA synthetase in complex with GDP-Mn2+
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JKJ PDB ENTRIES 1JKJ AND 1OI7 experimental model PDB 1OI7 PDB ENTRIES 1JKJ AND 1OI7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.4 294 10% PEG3350, 100 mM MES, 200 mM potassium chloride, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.87 57.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 261.7 α = 90 b = 126.8 β = 112.76 c = 110.6 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 ADSC QUANTUM 210 2005-10-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.1159 ALS 8.3.1
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 2.35 200 86.7 0.129 8.8 120106 120106
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 2.35 2.39 49.3 0.414 3383
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 (All) 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 PDB ENTRIES 1JKJ AND 1OI7 2.35 50.994 1.35 120106 120075 6048 86.73 0.2075 0.2062 0.2042 0.191 0.2452 0.2319 RANDOM 42.4683
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] 10.4611 7.1564 -10.7743 0.3133
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.799 f_angle_d 1.041 f_chiral_restr 0.064 f_bond_d 0.008 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 19696 Nucleic Acid Atoms Solvent Atoms 735 Heterogen Atoms 116
Software Software Software Name Purpose SCALEPACK data scaling AMoRE phasing PHENIX refinement PDB_EXTRACT data extraction ADSC data collection DENZO data reduction