☰ Navigation Tabs
COMPLEX STRUCTURE OF CDYL2 WITH AN ANTAGONIST
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4HAE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 291 25.0% PEG3350, 0.2M NH4OAc, 0.1M Bis-Tris, pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.57 47.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.905 α = 90 b = 88.576 β = 90 c = 113.237 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 2021-11-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.9792 APS 24-ID-E
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 1.45 50 97.6 0.061 0.065 0.021 0.998 8.2 9 80579
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 1.45 1.48 92.1 0.787 0.854 0.323 0.76 6.7
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 4HAE 1.45 47.75 76362 4152 97.53 0.21558 0.2144 0.2237 0.23637 0.2421 RANDOM 19.483
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] 0.41 0.27 -0.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.125 r_dihedral_angle_3_deg 12.747 r_dihedral_angle_4_deg 11.261 r_dihedral_angle_1_deg 6.979 r_long_range_B_refined 4.623 r_long_range_B_other 4.487 r_scangle_other 2.579 r_mcangle_it 2.378 r_mcangle_other 2.378 r_scbond_it 1.607
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.125 r_dihedral_angle_3_deg 12.747 r_dihedral_angle_4_deg 11.261 r_dihedral_angle_1_deg 6.979 r_long_range_B_refined 4.623 r_long_range_B_other 4.487 r_scangle_other 2.579 r_mcangle_it 2.378 r_mcangle_other 2.378 r_scbond_it 1.607 r_scbond_other 1.606 r_mcbond_it 1.467 r_mcbond_other 1.461 r_angle_refined_deg 1.334 r_angle_other_deg 1.254 r_chiral_restr 0.064 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2850 Nucleic Acid Atoms Solvent Atoms 415 Heterogen Atoms 367
Software Software Software Name Purpose REFMAC refinement HKL-3000 data scaling PHASER phasing