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Human CtBP2(31-364) in complex with RAI2 peptide(315-322)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OME 2OME
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 277.15 20% PEG 6000, 100 mM Tris pH 7.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 126.646 α = 90 b = 126.646 β = 90 c = 357.598 γ = 120
Symmetry Space Group P 61 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 291 PIXEL DECTRIS PILATUS 6M-F 2018-12-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.976243 PETRA III, EMBL c/o DESY P13 (MX1)
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 2.6 50 99.9 0.03685 0.05211 0.99 12.87 2 53115 55.96
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.693 100 0.4276 0.6048 1.8
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2OME 2.6 49.869 53114 2633 99.91 0.231 0.2283 0.2283 0.2833 0.2837 77.187
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] 0.041 0.021 0.041 -0.133
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.53 r_dihedral_angle_6_deg 14.81 r_lrange_it 9.85 r_dihedral_angle_2_deg 7.976 r_dihedral_angle_1_deg 7.308 r_scangle_it 6.919 r_mcangle_it 5.737 r_scbond_it 4.651 r_mcbond_it 3.743 r_angle_refined_deg 1.779
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.53 r_dihedral_angle_6_deg 14.81 r_lrange_it 9.85 r_dihedral_angle_2_deg 7.976 r_dihedral_angle_1_deg 7.308 r_scangle_it 6.919 r_mcangle_it 5.737 r_scbond_it 4.651 r_mcbond_it 3.743 r_angle_refined_deg 1.779 r_nbtor_refined 0.307 r_symmetry_nbd_refined 0.226 r_nbd_refined 0.219 r_symmetry_xyhbond_nbd_refined 0.21 r_xyhbond_nbd_refined 0.167 r_chiral_restr 0.122 r_ncsr_local_group_6 0.106 r_ncsr_local_group_5 0.104 r_ncsr_local_group_3 0.102 r_ncsr_local_group_4 0.092 r_ncsr_local_group_2 0.086 r_ncsr_local_group_1 0.073 r_bond_refined_d 0.008 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10357 Nucleic Acid Atoms Solvent Atoms 206 Heterogen Atoms 183
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALEPACK data scaling PHASER phasing PDB_EXTRACT data extraction