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Structure of T4 RNA Ligase 2 with Nicked 5'-Adenylated nucleic acid duplex containing a 3'-deoxyribonucleotide at the nick
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HVQ PDB ENTRY 2HVQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 295 100 mM Bis-Tris, 22% PEG-4000, 9% PEG-6000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.6 52.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.569 α = 90 b = 106.16 β = 90 c = 125.329 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 100 CCD ADSC QUANTUM 4 2005-11-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.9790 APS 24-ID-C
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 2.45 20 99 0.066 17.7 5.7 41628 41212
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) 2.45 2.54 97.5 0.372 2.7 3.7 3990
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (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 THROUGHOUT PDB ENTRY 2HVQ 2.45 19.92 41572 41156 2056 99 0.236 0.2377 0.295 0.2973 RANDOM 64.9
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] -13.03 9.12 3.9
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21.1 c_scangle_it 5.72 c_mcangle_it 3.71 c_scbond_it 3.69 c_mcbond_it 2.31 c_angle_deg 1.2 c_improper_angle_d 0.98 c_bond_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5042 Nucleic Acid Atoms 2006 Solvent Atoms 129 Heterogen Atoms 42
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling CNS refinement PDB_EXTRACT data extraction MOLREP phasing