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ARID1B ARID bound to compound B-2 ((2M)-2'-(morpholin-4-yl)-6-oxo-4-(trifluoromethyl)-1,6-dihydro[2,3'-bipyridine]-5-carbonitrile)
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 10.7% PEG3350, 0.044 M zinc acetate, 0.025% w/v 3,5-dinitrosalicylic acid, 0.025% w/v 4-aminobenzoic acid, 0.025% w/v salicylic acid, 0.025% w/v trimesic acid, 0.002 M HEPES sodium, pH 6.8
Crystal Properties Matthews coefficient Solvent content 2.85 56.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.32 α = 90 b = 90.32 β = 90 c = 37.74 γ = 90
Symmetry Space Group P 4 21 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 S 6M 2023-10-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.11584 ALS 8.3.1
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 1.88 64.04 99.65 0.123 0.031 0.999 13.5 16.28 13242 33.3
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 1.88 1.95 99.22 2.067 0.592 1.2 15.61
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 1.88 63.87 1.34 13210 1321 99.95 0.2047 0.2004 0.2049 0.2451 0.2454 38.15
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 19.508 f_angle_d 1.228 f_chiral_restr 0.0503 f_plane_restr 0.0148 f_bond_d 0.0112
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 803 Nucleic Acid Atoms Solvent Atoms 56 Heterogen Atoms 43
Software Software Software Name Purpose PHENIX refinement autoPROC data reduction XSCALE data scaling PHASER phasing