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Crystal Structure of chromodomain of CDYL in complex with inhibitor UNC6261
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6V41
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 291 3.5M Na Formate, 0.1M Bis-Tris propane pH7.0
Crystal Properties Matthews coefficient Solvent content 2.01 38.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.971 α = 90 b = 76.386 β = 90 c = 80.628 γ = 90
Symmetry Space Group P 21 21 21
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 EIGER X 16M 2019-07-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.97934 APS 24-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.84 50 99.3 0.083 10.5 5.9 33365
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.84 1.87 98.8 0.752 4.2
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 6V41 1.85 48.64 31770 1542 98.4 0.227 0.225 0.2328 0.262 0.2705 RANDOM 31.01
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] 1.86 -2.27 0.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.616 r_dihedral_angle_4_deg 17.014 r_dihedral_angle_3_deg 14.239 r_dihedral_angle_1_deg 6.938 r_angle_other_deg 2.427 r_angle_refined_deg 1.572 r_chiral_restr 0.063 r_bond_refined_d 0.014 r_bond_other_d 0.009 r_gen_planes_refined 0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.616 r_dihedral_angle_4_deg 17.014 r_dihedral_angle_3_deg 14.239 r_dihedral_angle_1_deg 6.938 r_angle_other_deg 2.427 r_angle_refined_deg 1.572 r_chiral_restr 0.063 r_bond_refined_d 0.014 r_bond_other_d 0.009 r_gen_planes_refined 0.006 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3191 Nucleic Acid Atoms Solvent Atoms 69 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement HKL-3000 data scaling PDB_EXTRACT data extraction PHASER phasing HKL-3000 data reduction