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Crystal structure of the second bromodomain H395R mutant of human BRD3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OO1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277 0.2 M sodium nitrate, 10 % PEG 3350, 5 % EDO, 0.1 M bis tris prop. pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.97 58.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.828 α = 90 b = 92.546 β = 90 c = 102.954 γ = 90
Symmetry Space Group P 21 2 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 2014-07-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
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 29.55 99.3 0.234 0.07 13 12.7 68935 68935
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 87.4 2.483 2.7 10.3
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 2OO1 1.7 29.55 65516 3348 99.26 0.195 0.19369 0.2048 0.22086 0.2335 RANDOM 20.09
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] -1.01 -0.4 1.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.808 r_dihedral_angle_4_deg 19.98 r_dihedral_angle_3_deg 11.724 r_long_range_B_refined 5.109 r_long_range_B_other 5.109 r_dihedral_angle_1_deg 5.082 r_scangle_other 3.149 r_scbond_it 1.987 r_scbond_other 1.984 r_mcangle_other 1.736
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.808 r_dihedral_angle_4_deg 19.98 r_dihedral_angle_3_deg 11.724 r_long_range_B_refined 5.109 r_long_range_B_other 5.109 r_dihedral_angle_1_deg 5.082 r_scangle_other 3.149 r_scbond_it 1.987 r_scbond_other 1.984 r_mcangle_other 1.736 r_mcangle_it 1.735 r_angle_refined_deg 1.486 r_mcbond_it 1.111 r_mcbond_other 1.108 r_angle_other_deg 0.86 r_chiral_restr 0.09 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_bond_other_d 0.001 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 3628 Nucleic Acid Atoms Solvent Atoms 402 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing