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Crystal Structure of C. Thermocellum PNKP Ligase Domain AMP-Adenylate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3TY5 PDB 3TY5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.1 295 HEPES buffer 20% (v/v) Hexylene Glycol, pH 7.1, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.86 56.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.5 α = 90 b = 132.76 β = 90 c = 162.77 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 130 PIXEL DECTRIS PILATUS 6M See Beamline Documentation 2011-02-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 1.1 NSLS X25
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 3.12 50 99.8 0.065 9.2 7.3 37602 37527 -3
Refinement Statistics Diffraction ID Structure Solution 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 PDB 3TY5 3.12 41.185 1.38 37457 1669 99.78 0.221 0.2189 0.2113 0.2663 0.2515 random
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] 51.8235 -22.0948 -21.6232
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 15.174 f_angle_d 0.851 f_chiral_restr 0.059 f_bond_d 0.005 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12022 Nucleic Acid Atoms Solvent Atoms 52 Heterogen Atoms 226
Software Software Software Name Purpose CBASS data collection PHENIX model building PHENIX refinement MOSFLM data reduction SCALA data scaling PHENIX phasing