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Crystal structure of human BRD9 bromodomain in complex with LP99 chemical probe
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HME
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277 0.2 M sodium nitrate, 0.1 M bis tris propane pH 8.5, 20% PEG 3350, 10% ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.1 41.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 28.527 α = 90 b = 39.496 β = 90 c = 212.439 γ = 90
Symmetry Space Group P 21 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 PIXEL DECTRIS PILATUS 6M 2014-07-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.9795 Diamond I02
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 1.7 28.93 99.8 0.126 0.045 15.5 9.6 27716 6.873
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 1.7 1.73 97.3 0.708 3.2 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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3HME 1.7 28.93 26282 1357 99.74 0.21214 0.21054 0.24282 0.2328 RANDOM 16.157
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] 1.02 -1 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.014 r_dihedral_angle_4_deg 18.839 r_dihedral_angle_3_deg 13.167 r_dihedral_angle_1_deg 4.272 r_long_range_B_refined 4.025 r_long_range_B_other 3.88 r_scangle_other 2.306 r_angle_refined_deg 1.661 r_scbond_it 1.428 r_scbond_other 1.427
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.014 r_dihedral_angle_4_deg 18.839 r_dihedral_angle_3_deg 13.167 r_dihedral_angle_1_deg 4.272 r_long_range_B_refined 4.025 r_long_range_B_other 3.88 r_scangle_other 2.306 r_angle_refined_deg 1.661 r_scbond_it 1.428 r_scbond_other 1.427 r_mcangle_it 1.196 r_mcangle_other 1.195 r_angle_other_deg 0.937 r_mcbond_it 0.743 r_mcbond_other 0.743 r_chiral_restr 0.086 r_bond_refined_d 0.014 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1840 Nucleic Acid Atoms Solvent Atoms 178 Heterogen Atoms 70
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing