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Crystal structure of CtBP2 in complex with G9a
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8ATI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 291 0.1 M HEPES pH 7.5, 6% PVP, 30% pentaerythritol ethoxylate
Crystal Properties Matthews coefficient Solvent content 2.79 55.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 178.126 α = 90 b = 178.126 β = 90 c = 138.833 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 PIXEL DECTRIS EIGER2 S 9M 2024-07-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL02U1 0.91990 SSRF BL02U1
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 1.85 50 100 0.157 0.161 0.038 0.997 5.3 17.1 71788
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 1.85 1.88 100 1.662 1.754 0.552 0.551 10
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.85 41.1 68146 3640 99.92 0.16866 0.16696 0.20158 0.1862 RANDOM 30.026
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] -0.32 -0.16 -0.32 1.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.84 r_dihedral_angle_2_deg 9.444 r_long_range_B_refined 8.259 r_long_range_B_other 8.21 r_dihedral_angle_1_deg 6.785 r_scangle_other 6.708 r_scbond_it 4.322 r_scbond_other 4.312 r_mcangle_it 3.732 r_mcangle_other 3.732
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.84 r_dihedral_angle_2_deg 9.444 r_long_range_B_refined 8.259 r_long_range_B_other 8.21 r_dihedral_angle_1_deg 6.785 r_scangle_other 6.708 r_scbond_it 4.322 r_scbond_other 4.312 r_mcangle_it 3.732 r_mcangle_other 3.732 r_mcbond_it 2.831 r_mcbond_other 2.829 r_angle_refined_deg 1.597 r_angle_other_deg 0.545 r_chiral_restr 0.076 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 5280 Nucleic Acid Atoms Solvent Atoms 660 Heterogen Atoms 88
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling HKL-2000 data reduction PHASER phasing PDB_EXTRACT data extraction