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G-059 bound to the SMARCA4 (BRG1) Bromodomain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7TAB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 277 Protein in buffer: 20 mM Hepes pH 7.5, 150 mM NaCl, 0.5 mM TCEP, at a concentration of 15.55 mg/ml (1.03 mM)
Reservoir solution contains: Jeffamine ED-2001 pH 7.0 at 30%, Tris-HCl pH 8.5 at 0.1 M, 5% v/v Ethyl acetate
Crystal Properties Matthews coefficient Solvent content 2.7 54.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.26 α = 90 b = 90.26 β = 90 c = 96.79 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 CCD RAYONIX MX-300 2013-09-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.9795 CLSI 08ID-1
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 1.61 50 100 0.074 9.9 9.3 57838
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 1.61 1.67 100 0.844 9.4
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 7TAB 1.61 41.147 57747 2933 99.874 0.208 0.2063 0.2064 0.2422 0.2424 29.413
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] 0.058 0.029 0.058 -0.189
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.588 r_dihedral_angle_4_deg 15.743 r_dihedral_angle_3_deg 14.785 r_lrange_it 6.606 r_scangle_it 5.922 r_dihedral_angle_1_deg 5.851 r_scbond_it 4.116 r_mcangle_it 3.199 r_mcbond_it 2.448 r_angle_refined_deg 1.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.588 r_dihedral_angle_4_deg 15.743 r_dihedral_angle_3_deg 14.785 r_lrange_it 6.606 r_scangle_it 5.922 r_dihedral_angle_1_deg 5.851 r_scbond_it 4.116 r_mcangle_it 3.199 r_mcbond_it 2.448 r_angle_refined_deg 1.96 r_nbtor_refined 0.318 r_nbd_refined 0.213 r_symmetry_nbd_refined 0.202 r_ncsr_local_group_2 0.137 r_ncsr_local_group_3 0.136 r_ncsr_local_group_1 0.118 r_chiral_restr 0.113 r_symmetry_xyhbond_nbd_refined 0.104 r_xyhbond_nbd_refined 0.092 r_bond_refined_d 0.011 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2862 Nucleic Acid Atoms Solvent Atoms 229 Heterogen Atoms 60
Software Software Software Name Purpose SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction DENZO data reduction