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p300 KAT domain in complex with KB528
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BIY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 HM(PEGs-E9)-D6 (0.18M NH4Cl, 24% PEG 3350)
Crystal Properties Matthews coefficient Solvent content 2.56 52.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.4 α = 90 b = 164.933 β = 111.845 c = 56.588 γ = 90
Symmetry Space Group P 1 21 1
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 2024-07-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL45XU 0.99999 SPring-8 BL45XU
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 2 44.302 98 0.144 10 7.1 50921
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 2 2.05 1.085
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2 44.302 50870 2644 97.906 0.19 0.1878 0.1944 0.2378 0.2372 35.942
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] -1.279 0.951 0.293 0.169
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.372 r_dihedral_angle_3_deg 11.922 r_dihedral_angle_2_deg 7.166 r_lrange_it 6.61 r_lrange_other 6.55 r_dihedral_angle_1_deg 6.512 r_scangle_it 4.867 r_scangle_other 4.866 r_mcangle_it 3.772 r_mcangle_other 3.772
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.372 r_dihedral_angle_3_deg 11.922 r_dihedral_angle_2_deg 7.166 r_lrange_it 6.61 r_lrange_other 6.55 r_dihedral_angle_1_deg 6.512 r_scangle_it 4.867 r_scangle_other 4.866 r_mcangle_it 3.772 r_mcangle_other 3.772 r_scbond_it 3.03 r_scbond_other 3.029 r_mcbond_it 2.506 r_mcbond_other 2.505 r_angle_refined_deg 1.281 r_angle_other_deg 0.464 r_nbd_refined 0.202 r_nbd_other 0.198 r_symmetry_xyhbond_nbd_refined 0.192 r_symmetry_nbd_other 0.185 r_nbtor_refined 0.179 r_symmetry_nbd_refined 0.174 r_xyhbond_nbd_refined 0.166 r_symmetry_nbtor_other 0.076 r_chiral_restr 0.065 r_chiral_restr_other 0.041 r_symmetry_xyhbond_nbd_other 0.018 r_gen_planes_refined 0.005 r_bond_refined_d 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5380 Nucleic Acid Atoms Solvent Atoms 478 Heterogen Atoms 92
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing