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The C-terminal glycosylase domain of human MBD4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 25% PEG3350, 0.2M Li Sulfate, 0.1M Hepes pH 7.5, VAPOR DIFFUSION, SITTING DROP
Crystal Properties Matthews coefficient Solvent content 2.99 58.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.541 α = 90 b = 83.541 β = 90 c = 73.956 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID APS 19-ID
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 2.697 51.71 93.7 0.09 6.3 3.7 5287
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 2.697 2.8 64.3 0.315 2.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.7 51.71 4589 218 90.85 0.18735 0.18248 0.1807 0.29003 0.2857 RANDOM 24.405
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] 1.89 0.94 1.89 -2.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.271 r_dihedral_angle_4_deg 18.907 r_dihedral_angle_3_deg 18.877 r_dihedral_angle_1_deg 6.489 r_scangle_it 4.228 r_scbond_it 2.544 r_angle_refined_deg 1.978 r_mcangle_it 1.61 r_mcbond_it 0.804 r_chiral_restr 0.125
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.271 r_dihedral_angle_4_deg 18.907 r_dihedral_angle_3_deg 18.877 r_dihedral_angle_1_deg 6.489 r_scangle_it 4.228 r_scbond_it 2.544 r_angle_refined_deg 1.978 r_mcangle_it 1.61 r_mcbond_it 0.804 r_chiral_restr 0.125 r_bond_refined_d 0.021 r_gen_planes_refined 0.01 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 1146 Nucleic Acid Atoms Solvent Atoms 12 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction