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Crystal Structure of T4 Pyrimidine Dimer Glycosylase (T4-Pdg) Covalently Complexed with a DNA Substrate Containing Abasic Site
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VAS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.4 293 2 M (NH4)2SO4 and 0.1 M sodium citrate buffer (pH 6.4), VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 184.059 α = 90 b = 184.059 β = 90 c = 100.855 γ = 120
Symmetry Space Group P 64 2 2
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 2002-08-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X26C 0.9188 NSLS X26C
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 2.3 40 99.6 0.068 11.5 5.9 81403 21.6
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 2.3 2.34 99.2 0.393
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1VAS 2.3 39.85 81403 4032 96.1 0.249 0.249 0.274 0.2679 RANDOM 41
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] 2.36 0.6 2.36 -4.72
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 20.5 c_scangle_it 3.19 c_scbond_it 2.12 c_mcangle_it 1.95 c_mcbond_it 1.21 c_angle_deg 1.1 c_improper_angle_d 1.05 c_bond_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2254 Nucleic Acid Atoms 1036 Solvent Atoms 183 Heterogen Atoms 22
Software Software Software Name Purpose CNS refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing