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Crystal structure of CtBP1 in complex with PALI1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9WRI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 291 30% pentaerythritol ethoxylate, 0.1 M magnesium formate dihydrate, 0.1 M Tris pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.31 46.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.869 α = 90 b = 88.869 β = 90 c = 165.087 γ = 120
Symmetry Space Group P 64 2 2
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 PILATUS3 6M 2024-10-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.97861 SSRF BL19U1
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 2.2 50 99.4 0.159 0.163 0.999 17.11 17.88 20286
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 2.2 2.33 98.3 2.968 3.701 0.298 1.01 10.4
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.2 44.76 19270 1015 99.41 0.20261 0.19945 0.2072 0.26192 0.2707 RANDOM 56.411
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] 0.72 0.36 0.72 -2.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.969 r_long_range_B_other 10.09 r_long_range_B_refined 10.086 r_scangle_other 8.327 r_dihedral_angle_2_deg 7.9 r_dihedral_angle_1_deg 7.208 r_mcangle_it 6.468 r_mcangle_other 6.466 r_scbond_it 5.885 r_scbond_other 5.883
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.969 r_long_range_B_other 10.09 r_long_range_B_refined 10.086 r_scangle_other 8.327 r_dihedral_angle_2_deg 7.9 r_dihedral_angle_1_deg 7.208 r_mcangle_it 6.468 r_mcangle_other 6.466 r_scbond_it 5.885 r_scbond_other 5.883 r_mcbond_it 4.969 r_mcbond_other 4.96 r_angle_refined_deg 1.629 r_angle_other_deg 0.566 r_chiral_restr 0.081 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 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 2610 Nucleic Acid Atoms Solvent Atoms 61 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement XDS data scaling XDS data reduction PHASER phasing PDB_EXTRACT data extraction