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Crystal structure of CDYL2 in complex with H3tK27me3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6V41 an early version of PDB entry 6V41 (CDY1 in complex with a histone peptide)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 277 23% PEG3350, 0.25 M ammonium dihydrogen phosphate, 0.1 M sodium cacodylate
Crystal Properties Matthews coefficient Solvent content 5.49 77.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 210.75 α = 90 b = 210.75 β = 90 c = 67.2 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 CCD MARMOSAIC 300 mm CCD 2015-01-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.97957 CLSI 08ID-1
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 63.06 100 0.099 0.109 0.045 0.997 14.8 5.9 34195
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 2.67 100 0.997 1.095 0.452 0.658 5.9
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT an early version of PDB entry 6V41 (CDY1 in complex with a histone peptide) 2.6 63.14 31961 2234 99.97 0.2185 0.2173 0.2233 0.2366 0.2414 58.187
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] -0.6 -0.3 -0.6 1.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.67 r_dihedral_angle_3_deg 14.703 r_dihedral_angle_4_deg 12.522 r_dihedral_angle_1_deg 5.394 r_angle_refined_deg 1.362 r_angle_other_deg 0.911 r_chiral_restr 0.079 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.67 r_dihedral_angle_3_deg 14.703 r_dihedral_angle_4_deg 12.522 r_dihedral_angle_1_deg 5.394 r_angle_refined_deg 1.362 r_angle_other_deg 0.911 r_chiral_restr 0.079 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3322 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction xia2 data reduction PHASER phasing