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Crystal Structure of MutY bound to its inhibitor DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RRQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 277 Tris, PEG4000 calcium acetate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.45 49.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.7 α = 90 b = 85.9 β = 90 c = 142.1 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 IMAGE PLATE RIGAKU RAXIS V 2008-04-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E APS 24-ID-E
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 2.2 50 99.9 0.088 39.75 6.8 24152
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) 2.2 2.28 100 0.472 7.2
Refinement Statistics Diffraction ID Structure Solution 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 Selection Details Mean Isotropic B X-RAY DIFFRACTION 1RRQ 2.2 50 23458 2328 96.6 0.246 0.246 0.2407 0.277 RANDOM 61.292
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] -2.112 -3.717 5.83
RMS Deviations Key Refinement Restraint Deviation c_scangle_it 3.873 c_mcangle_it 2.993 c_scbond_it 2.478 c_mcbond_it 1.774 c_bond_d c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot
RMS Deviations Key Refinement Restraint Deviation c_scangle_it 3.873 c_mcangle_it 2.993 c_scbond_it 2.478 c_mcbond_it 1.774 c_bond_d c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2760 Nucleic Acid Atoms 428 Solvent Atoms 42 Heterogen Atoms 9
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling CNS refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction CNS phasing