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Crystal structure of Thermosynechococcus elongatus Lipoyl Synthase 2 complexed with MTA and DTT
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4U0P
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 100 mM bicine pH 8.5, 15% PEG 20,000, 3% dextran sulfate sodium salt
Crystal Properties Matthews coefficient Solvent content 2.74 55.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.88 α = 90 b = 162.8 β = 90 c = 58.6 γ = 90
Symmetry Space Group C 2 2 21
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 PSI PILATUS 6M 2013-02-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.97950 Diamond I02
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.6 64.99 98.2 0.037 0.025 15 4.4 44264 27.38
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.64 98.6 0.601 0.362 2.1 4.7 3268
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 4U0P 1.6 64.988 1.33 44172 2229 97.78 0.2045 0.2027 0.2068 0.2415 0.2469 Random selection 36.78
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 14.224 f_angle_d 1.958 f_chiral_restr 0.085 f_bond_d 0.017 f_plane_restr 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2055 Nucleic Acid Atoms Solvent Atoms 181 Heterogen Atoms 69
Software Software Software Name Purpose Coot model building PDB_EXTRACT data extraction PHASER phasing PHENIX refinement XDS data reduction SCALA data scaling xia2 data scaling