☰ Navigation Tabs
crystal structure of CDY1 chromodomain bound to H3K9me3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4HAE pdb entry 4hae
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 291 1.4 M sodium citrate, 0.1 M HEPES
Crystal Properties Matthews coefficient Solvent content 1.81 32.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.447 α = 90 b = 42.447 β = 90 c = 37.195 γ = 90
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 RIGAKU SATURN A200 2014-09-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.6 23.36 99.9 0.028 0.03 1 43.4 7 8814
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.6 1.63 99.1 0.371 0.403 0.914 6.6
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 (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE pdb entry 4hae 1.603 23.301 8794 411 99.955 0.193 0.1917 0.215 0.2099 22.062
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] 0.253 0.253 -0.505
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.417 r_dihedral_angle_3_deg 15.351 r_dihedral_angle_4_deg 13.818 r_dihedral_angle_1_deg 6.416 r_lrange_it 4.516 r_lrange_other 4.457 r_scangle_it 2.7 r_scangle_other 2.698 r_angle_refined_deg 2.005 r_mcangle_it 1.937
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.417 r_dihedral_angle_3_deg 15.351 r_dihedral_angle_4_deg 13.818 r_dihedral_angle_1_deg 6.416 r_lrange_it 4.516 r_lrange_other 4.457 r_scangle_it 2.7 r_scangle_other 2.698 r_angle_refined_deg 2.005 r_mcangle_it 1.937 r_mcangle_other 1.925 r_scbond_it 1.771 r_scbond_other 1.769 r_angle_other_deg 1.491 r_mcbond_it 1.323 r_mcbond_other 1.321 r_nbd_refined 0.282 r_symmetry_nbd_refined 0.239 r_nbd_other 0.229 r_symmetry_nbd_other 0.208 r_symmetry_xyhbond_nbd_refined 0.184 r_nbtor_refined 0.168 r_xyhbond_nbd_refined 0.092 r_chiral_restr 0.091 r_symmetry_nbtor_other 0.083 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 586 Nucleic Acid Atoms Solvent Atoms 20 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing