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Crystal structure of the bromodomain of the human ATAD2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OSS PDB entry 2OSS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 277 2M (NH4)2SO4, 0.1M Bis-Tris pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 4.07 69.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.616 α = 90 b = 79.616 β = 90 c = 137.55 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 2008-04-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.54178
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.95 39.81 99.9 0.085 0.085 20.5 10.8 19492
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2.06 99.7 0.779 0.779 2.9 9.9
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-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 entry 2OSS 1.95 39.81 19461 1000 99.86 0.203 0.203 0.201 0.2045 0.24 0.2462 RANDOM 23.193
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] 0.23 0.12 0.23 -0.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.626 r_dihedral_angle_4_deg 21.22 r_dihedral_angle_3_deg 15.034 r_scangle_it 9.649 r_scbond_it 7.377 r_dihedral_angle_1_deg 4.803 r_mcangle_it 4.798 r_mcbond_it 3.394 r_angle_refined_deg 1.316 r_angle_other_deg 1.052
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.626 r_dihedral_angle_4_deg 21.22 r_dihedral_angle_3_deg 15.034 r_scangle_it 9.649 r_scbond_it 7.377 r_dihedral_angle_1_deg 4.803 r_mcangle_it 4.798 r_mcbond_it 3.394 r_angle_refined_deg 1.316 r_angle_other_deg 1.052 r_mcbond_other 1.02 r_chiral_restr 0.087 r_bond_refined_d 0.016 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1064 Nucleic Acid Atoms Solvent Atoms 161 Heterogen Atoms 11
Software Software Software Name Purpose SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection MOSFLM data reduction