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Crystal structure of MutT-8-OXO-DGMP complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3A6S PDB ENTRY 3A6S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 288 2.0M AMMONIUM SULFATE, 0.2M POTASSIUM SODIUM TARTRATE, 0.1M TRISODIUM CITRATE, pH 5.60, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Crystal Properties Matthews coefficient Solvent content 2.11 41.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.972 α = 90 b = 56.007 β = 90 c = 59.369 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 MARRESEARCH 2003-02-15 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD ADSC QUANTUM 4 2002-12-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 0.973 SPring-8 BL41XU 2 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1.0 SPring-8 BL38B1
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 1.96 20 97.6 0.065 29.6 5.8 9344 11.7
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) 1.96 2.08 93.2 0.181 6.2
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 3A6S 1.96 18.66 9280 499 97.3 0.178 0.178 0.1812 0.201 0.2029 RANDOM 18.7
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] 4.83 -1.94 -2.89
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.8 c_scangle_it 3.41 c_scbond_it 2.25 c_mcangle_it 2 c_angle_deg 1.3 c_mcbond_it 1.3 c_improper_angle_d 0.81 c_bond_d 0.005 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.8 c_scangle_it 3.41 c_scbond_it 2.25 c_mcangle_it 2 c_angle_deg 1.3 c_mcbond_it 1.3 c_improper_angle_d 0.81 c_bond_d 0.005 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 1038 Nucleic Acid Atoms Solvent Atoms 136 Heterogen Atoms 58
Software Software Software Name Purpose AMoRE phasing CNS refinement HKL-2000 data reduction SCALEPACK data scaling