☰ Navigation Tabs
Structure of the bromodomain of human ATPase family AAA domain-containing protein 2 (ATAD2) with bound MPD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DAI pdb id: 3DAI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 277.15 apo crystals grew in 1.8-2.2 M ammonium sulphate, 0.1 M Bis-Tris, pH 5.5-6.5. Soaking performed in 45-50% MPD, 0.1 M bis-tris pH 5.5, 0.1 M ammonium phosphate, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K
Crystal Properties Matthews coefficient Solvent content 4.12 70.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.584 α = 90 b = 79.584 β = 90 c = 139.363 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 IMAGE PLATE RIGAKU RAXIS IV 2011-12-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.5418
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 2 19.26 98.8 0.134 12.5 5.7 18063 18053 21.7
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 2 2.11 95.6 0.86 2 5.5 2489
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 pdb id: 3DAI 2 19.26 2 18053 17126 927 98.38 0.193 0.15999 0.15794 0.1637 0.19844 0.1995 RANDOM 31.937
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] -0.61 -0.31 -0.61 0.92
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.892 r_dihedral_angle_3_deg 13.284 r_dihedral_angle_4_deg 11.533 r_dihedral_angle_1_deg 4.907 r_angle_refined_deg 1.641 r_angle_other_deg 0.97 r_chiral_restr 0.098 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.892 r_dihedral_angle_3_deg 13.284 r_dihedral_angle_4_deg 11.533 r_dihedral_angle_1_deg 4.907 r_angle_refined_deg 1.641 r_angle_other_deg 0.97 r_chiral_restr 0.098 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1084 Nucleic Acid Atoms Solvent Atoms 198 Heterogen Atoms 40
Software Software Software Name Purpose CrystalClear data collection PHASER phasing REFMAC refinement XDS data reduction SCALA data scaling