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Crystal Structure of Human THYN1 protein in complex with 5-methylcytosine containing DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3EOP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 293 0.1M TRISODIUM CITRATE, 0.2M NaCl, 30% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.41 49.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.327 α = 90 b = 73.232 β = 91.18 c = 108.201 γ = 90
Symmetry Space Group P 1 21 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 CCD ADSC QUANTUM 315r 2015-06-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97929 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.6 43.51 99.8 0.094 0.11 0.056 0.997 12.8 3.7 19516
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.72 100 0.729 0.85 0.435 0.764 2.1 3.8 2409
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 3EOP 2.6 43.51 18559 941 99.77 0.2106 0.2087 0.214 0.2488 0.2502 RANDOM 54.604
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] -0.43 1.34 -1.17 1.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.806 r_dihedral_angle_3_deg 14.834 r_dihedral_angle_4_deg 9.41 r_dihedral_angle_1_deg 6.787 r_mcangle_it 1.466 r_angle_refined_deg 1.379 r_angle_other_deg 1.078 r_mcbond_it 0.863 r_mcbond_other 0.859 r_chiral_restr 0.079
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.806 r_dihedral_angle_3_deg 14.834 r_dihedral_angle_4_deg 9.41 r_dihedral_angle_1_deg 6.787 r_mcangle_it 1.466 r_angle_refined_deg 1.379 r_angle_other_deg 1.078 r_mcbond_it 0.863 r_mcbond_other 0.859 r_chiral_restr 0.079 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_bond_other_d 0.004 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2728 Nucleic Acid Atoms 976 Solvent Atoms 10 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PHASER phasing PDB_EXTRACT data extraction XDS data reduction