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Structure of the glycosylase domain of MBD4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3IHO PDB ENTRY 3IHO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 298 30% PEG 4000, 100 mM Tris-HCl and 0.2 M MgCl2, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.42 49.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.97 α = 90 b = 80.97 β = 90 c = 74.56 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 100 PIXEL PSI PILATUS 6M 2011-06-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.9 SOLEIL PROXIMA 1
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 1.9 40.49 94 0.089 10.9 14328 13475 2 2 28.25
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 1.9 2.02 72 0.77 1.9 1661
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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3IHO 1.9 40.49 14328 13467 674 93.81 0.194 0.1928 0.1975 0.2182 0.2317 RANDOM 35.58
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] -7.0873 -7.0873 14.1745
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 17.83 t_omega_torsion 2.91 t_angle_deg 0.93 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_chiral_improper_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1197 Nucleic Acid Atoms Solvent Atoms 75 Heterogen Atoms
Software Software Software Name Purpose DNA data collection PHASER phasing BUSTER refinement XDS data reduction XDS data scaling