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ternary complex of DNA polymerase lambda of a two nucleotide gapped DNA substrate with a C in the scrunch site
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XSN PDB ENTRY 1XSN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 277 2M sodium formate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.99 58.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.249 α = 90 b = 68.386 β = 90 c = 137.108 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 RIGAKU SATURN 92 VariMax HF 2008-12-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
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 1.95 50 97.2 0.092 17.5 6.1 38282 38282 -3 -3 19.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.95 2.02 89.5 0.522 2.9 3.7 3479
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-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 THROUGHOUT PDB ENTRY 1XSN 1.95 24.32 38282 35934 1794 91.2 0.212 0.212 0.2027 0.233 0.2269 RANDOM 39.7
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] -9.68 13.42 -3.74
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21.6 c_scangle_it 4.2 c_scbond_it 3.59 c_mcangle_it 2.11 c_mcbond_it 1.32 c_angle_deg 1 c_improper_angle_d 0.89 c_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2528 Nucleic Acid Atoms 444 Solvent Atoms 331 Heterogen Atoms 37
Software Software Software Name Purpose StructureStudio data collection MOLREP phasing CNS refinement HKL-2000 data reduction HKL-2000 data scaling