☰ Navigation Tabs
Structural analysis of ING3 protein and its binding to histone H3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4AFL MrBump generates its own model for the molecular replacement from similarities with the PDB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.2 293 0.1 M phosphate-citrate buffer at pH 4.2, 10 % 2-propanol and 0.2 M Li2SO4
Crystal Properties Matthews coefficient Solvent content 2.75 55.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 149.394 α = 90 b = 149.394 β = 90 c = 149.394 γ = 90
Symmetry Space Group I 4 3 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 PILATUS 6M-F KB focusing mirrors 2022-11-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.979257 ALBA XALOC
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 2.91 74.69 95.7 0.08 0.081 0.011 1 41.4 73.9 6277 126.07
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 2.91 3 55.9 6.609 6.651 0.738 0.565 80.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.91 60.99 1.35 6276 627 95.64 0.2745 0.2696 0.2702 0.3154 0.3162 126.73
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 5.1355 f_angle_d 1.31 f_chiral_restr 0.0586 f_plane_restr 0.0143 f_bond_d 0.0095
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1702 Nucleic Acid Atoms Solvent Atoms 4 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement PHENIX refinement autoPROC data reduction autoPROC data scaling MrBUMP phasing