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Crystal Structure of CMD1 in complex with 5mC-DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7CY4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 290 15% (v/v) 2-propanol, 0.1 M sodium citrate, pH 5.0, and 10% (w/v) PEG 10000
Crystal Properties Matthews coefficient Solvent content 2.83 56.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 153.173 α = 90 b = 127.055 β = 102.74 c = 64.217 γ = 90
Symmetry Space Group C 1 2 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 PIXEL DECTRIS PILATUS3 S 6M 2020-05-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NFPSS BEAMLINE BL19U1 0.9785 NFPSS BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.1 50.01 96.6 0.069 1 18.6 6.7 62383
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.15 0.84 0.78 2.2
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 7CY4 2.1 50.01 59114 2987 88.95 0.1846 0.1824 0.1815 0.2273 0.2253 RANDOM 35.981
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] 2.52 -2.07 -2.32 0.67
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 45.089 r_dihedral_angle_2_deg 35.283 r_sphericity_bonded 30.685 r_dihedral_angle_4_deg 18.264 r_dihedral_angle_3_deg 14.774 r_dihedral_angle_1_deg 5.627 r_rigid_bond_restr 3.628 r_angle_refined_deg 1.179 r_chiral_restr 0.057 r_bond_refined_d 0.007
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 45.089 r_dihedral_angle_2_deg 35.283 r_sphericity_bonded 30.685 r_dihedral_angle_4_deg 18.264 r_dihedral_angle_3_deg 14.774 r_dihedral_angle_1_deg 5.627 r_rigid_bond_restr 3.628 r_angle_refined_deg 1.179 r_chiral_restr 0.057 r_bond_refined_d 0.007 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6633 Nucleic Acid Atoms 330 Solvent Atoms 438 Heterogen Atoms 72
Software Software Software Name Purpose XDS data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHENIX phasing