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Crystal structure of AtMBD6 with DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6C1A 6c1a, 2yk8 experimental model PDB 2YK8 6c1a, 2yk8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 291 0.1M Bis-tris pH 6.5, 25% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.53 51.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.316 α = 90 b = 40.316 β = 90 c = 83.824 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 DECTRIS EIGER X 16M 2021-07-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.9785 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 2.29 34.91 99.9 0.989 12.4 10.3 6926 75.32
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.29 2.37 98.9 0.644
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 6c1a, 2yk8 2.39 34.91 5757 303 99.93 0.2248 0.2233 0.2326 0.2535 0.2643 RANDOM 69.3496
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 24.682 r_dihedral_angle_4_deg 21.567 r_dihedral_angle_3_deg 17.14 r_dihedral_angle_1_deg 9.163 r_angle_refined_deg 1.693 r_angle_other_deg 1.468 CHIRAL-CENTER RESTRAINTS (A''3) 0.084 r_gen_planes_refined 0.011 r_bond_refined_d 0.008 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 24.682 r_dihedral_angle_4_deg 21.567 r_dihedral_angle_3_deg 17.14 r_dihedral_angle_1_deg 9.163 r_angle_refined_deg 1.693 r_angle_other_deg 1.468 CHIRAL-CENTER RESTRAINTS (A''3) 0.084 r_gen_planes_refined 0.011 r_bond_refined_d 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 395 Nucleic Acid Atoms 488 Solvent Atoms 20 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing