☰ Navigation Tabs
Physachenolide C with Bromodomain (BRD3-BD1)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3S91
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 10mM CaCl, 50mM Tris-HCl pH 8.5, 30% w/v PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.3 46.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.098 α = 90 b = 49.316 β = 90 c = 60.779 γ = 90
Symmetry Space Group P 2 21 21
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 ADSC QUANTUM 315r 2021-04-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.9792 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.8 44.1 94.55 0.064 0.076 0.998 13 5.8 12117 34.81
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 1.8 1.864 71.21 0.782 0.557 1.3 4.1
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3s91 1.8 44.1 11563 554 94.56 0.162 0.1584 0.1655 0.2353 0.2363 RANDOM 43.839
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] -2.21 1.24 0.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.925 r_dihedral_angle_3_deg 14.801 r_dihedral_angle_4_deg 6.536 r_dihedral_angle_1_deg 5.971 r_rigid_bond_restr 4.679 r_angle_refined_deg 2.285 r_angle_other_deg 1.558 r_chiral_restr 0.197 r_bond_refined_d 0.013 r_gen_planes_refined 0.009
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.925 r_dihedral_angle_3_deg 14.801 r_dihedral_angle_4_deg 6.536 r_dihedral_angle_1_deg 5.971 r_rigid_bond_restr 4.679 r_angle_refined_deg 2.285 r_angle_other_deg 1.558 r_chiral_restr 0.197 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_gen_planes_other 0.004 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 953 Nucleic Acid Atoms Solvent Atoms 58 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing