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Crystal Structure of CMD1 in complex with 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 2.8 56.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 153.613 α = 90 b = 125.764 β = 102.82 c = 64.034 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 2.15 50.01 96.7 0.067 1 15.8 6.6 60566
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 2.15 2.21 0.52 0.82 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 2.15 50.01 57529 3035 94.05 0.1896 0.1879 0.1885 0.2206 0.2189 RANDOM 40.4
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] 2.87 -0.62 -3.82 1.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.815 r_sphericity_free 26.609 r_sphericity_bonded 20.093 r_dihedral_angle_4_deg 19.479 r_dihedral_angle_3_deg 14.943 r_dihedral_angle_1_deg 5.596 r_rigid_bond_restr 3.986 r_angle_refined_deg 1.118 r_angle_other_deg 0.993 r_chiral_restr 0.055
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.815 r_sphericity_free 26.609 r_sphericity_bonded 20.093 r_dihedral_angle_4_deg 19.479 r_dihedral_angle_3_deg 14.943 r_dihedral_angle_1_deg 5.596 r_rigid_bond_restr 3.986 r_angle_refined_deg 1.118 r_angle_other_deg 0.993 r_chiral_restr 0.055 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6624 Nucleic Acid Atoms 327 Solvent Atoms 402 Heterogen Atoms 37
Software Software Software Name Purpose XDS data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHENIX phasing