☰ Navigation Tabs
ARID1B ARID bound to compound A-4 (N-[(5-methylthiophen-2-yl)methyl]-7,8-dihydro-5H-pyrano[4,3-b]pyridin-3-amine)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Internal model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 277 1.5 M sodium citrate, pH 6.5, 0.033% w/v 4-nitrobenzoic acid, 0.033% w/v 5-sulfosalicylic acid dihydrate, 0.033% w/v naphthalene-1,3,6-trisulfonic acid trisodium salt hydrate, 0.002 M HEPES sodium, pH 6.8
Crystal Properties Matthews coefficient Solvent content 2.31 46.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.759 α = 90 b = 68.759 β = 90 c = 45.712 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 EIGER X 9M 2023-08-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.953725 CLSI 08ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.2 36.26 99.97 0.056 0.013 0.999 27.4 20.14 38552 14.77
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.2 1.24 99.97 1.47 0.859 2.2 19.06
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 1.2 36.26 1.33 38516 1996 99.88 0.1903 0.1894 0.1893 0.2063 0.2065 19.23
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 16.0669 f_angle_d 0.8924 f_chiral_restr 0.0673 f_plane_restr 0.0062 f_bond_d 0.0061
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 877 Nucleic Acid Atoms Solvent Atoms 121 Heterogen Atoms 18
Software Software Software Name Purpose PHENIX refinement autoPROC data reduction XSCALE data scaling PHASER phasing