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Crystal structure analysis of the catalytic domain and interdomain connector of human MutY homologue
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MUY PDB Entry 1MUY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.9 298 20% PEG 3350, 0.2M Magnesium acetate, 0.005 M tris[2-carboxyethyl] phosphine (TCEP), 5% glycerol, 0.01 M spermidine, pH 7.9, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.44 49.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.311 α = 90 b = 82.167 β = 100.9 c = 63.46 γ = 90
Symmetry Space Group P 1 21 1
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 210 Si(111) channel-cut monochromator, toroidal focusing mirror 2007-04-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X6A 1.65 NSLS X6A
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 2.3 62.31 95.8 0.097 18.7 7.6 27002 25872
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) 2.3 2.36 93.4 0.437 4.6 7.8
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 SAD and Molecular Replacement THROUGHOUT PDB Entry 1MUY 2.3 62.31 27002 24674 1302 95.66 0.20843 0.20616 0.2113 0.25078 0.249 RANDOM 64.249
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] 2.45 -2.6 -5.43 2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.257 r_dihedral_angle_3_deg 15.363 r_dihedral_angle_4_deg 15.092 r_scangle_it 9.115 r_scbond_it 6.328 r_dihedral_angle_1_deg 5.891 r_mcangle_it 3.835 r_mcbond_it 2.459 r_angle_refined_deg 1.991 r_chiral_restr 0.159
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.257 r_dihedral_angle_3_deg 15.363 r_dihedral_angle_4_deg 15.092 r_scangle_it 9.115 r_scbond_it 6.328 r_dihedral_angle_1_deg 5.891 r_mcangle_it 3.835 r_mcbond_it 2.459 r_angle_refined_deg 1.991 r_chiral_restr 0.159 r_bond_refined_d 0.017 r_gen_planes_refined 0.009 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4037 Nucleic Acid Atoms Solvent Atoms 55 Heterogen Atoms 19
Software Software Software Name Purpose HKL-2000 data collection MLPHARE phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling