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XChem fragment screen -- CRYSTAL STRUCTURE OF THE BROMODOMAIN OF THE HUMAN ATAD2 in complex with N13413a
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DAI 3DAI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 277 2.2M ammonium sulfate, 0.1M bis-tris pH 5.5
Crystal Properties Matthews coefficient Solvent content 4.2 70.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.79 α = 90 b = 80.79 β = 90 c = 140.36 γ = 120
Symmetry Space Group P 65 2 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 2015-11-21 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92819 Diamond I04-1
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 1.4 70.18 100 0.07 0.072 0.017 1 24.8 17.5 53979
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 1.4 1.44 99.9 2.034 2.124 0.603 0.471 12.2 3908
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 FOURIER SYNTHESIS THROUGHOUT 3DAI 1.4 49.6 51181 2720 99.94 0.1332 0.1319 0.1322 0.1589 0.1594 RANDOM 23.542
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] 0.28 0.14 0.28 -0.92
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.584 r_dihedral_angle_4_deg 16.001 r_dihedral_angle_3_deg 11.802 r_dihedral_angle_1_deg 4.629 r_rigid_bond_restr 4.116 r_mcangle_it 3.22 r_mcbond_it 2.649 r_mcbond_other 2.649 r_angle_refined_deg 1.888 r_angle_other_deg 1.523
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.584 r_dihedral_angle_4_deg 16.001 r_dihedral_angle_3_deg 11.802 r_dihedral_angle_1_deg 4.629 r_rigid_bond_restr 4.116 r_mcangle_it 3.22 r_mcbond_it 2.649 r_mcbond_other 2.649 r_angle_refined_deg 1.888 r_angle_other_deg 1.523 r_chiral_restr 0.098 r_bond_refined_d 0.017 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1084 Nucleic Acid Atoms Solvent Atoms 232 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing