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Complex structure of Sulfolobus solfataricus DPO4 and DNA duplex containing a hydrophobic thymine isostere 2,4-difluorotoluene nucleotide in the template strand
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2UVV PDB ENTRY 2UVV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 30 MM NACL, 2%GLYCEROL, 10 MM TRIS PH 7.5, 2.5 MM CACL2, 0.5 MM DDCTP, 6% PEG 3350, 0.05 CALCIUM ACETATE
Crystal Properties Matthews coefficient Solvent content 2.68 54.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.62 α = 90 b = 103.566 β = 90 c = 52.645 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 CCD ADSC CCD PT-COATED TOROIDAL MIRROR 2007-05-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 NSLS X25
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 2.98 30.17 84.5 0.09 14.3 3.3 9628 1 77.5
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 2.98 3.09 81 0.3 4.05 2
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2UVV 2.98 30.17 9358 500 84.5 0.231 0.231 0.217 0.282 0.258 RANDOM 58.8
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] 7.8 -3.82 -3.99
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23 c_scangle_it 3.03 c_mcangle_it 2.29 c_angle_deg 1.8 c_scbond_it 1.78 c_improper_angle_d 1.3 c_mcbond_it 1.28 c_bond_d 0.011 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23 c_scangle_it 3.03 c_mcangle_it 2.29 c_angle_deg 1.8 c_scbond_it 1.78 c_improper_angle_d 1.3 c_mcbond_it 1.28 c_bond_d 0.011 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2753 Nucleic Acid Atoms 591 Solvent Atoms 63 Heterogen Atoms 34
Software Software Software Name Purpose CNS refinement HKL-2000 data reduction HKL-2000 data scaling CNS phasing