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Crystal structure of the bromodomain of human BRD1 (BRPF2) in complex with OF-1 chemical probe
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3RCW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277.15 0.1 M tri-sodium citrate dihydrate pH 5.6, 1 M ammoinum dihydrogen phosphate
Crystal Properties Matthews coefficient Solvent content 2.62 53.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.771 α = 90 b = 84.328 β = 90 c = 52.08 γ = 90
Symmetry Space Group C 2 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 2014-07-12 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 1.1 29.27 97.9 0.07 0.034 22 9.1 62094 62094 8.788
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 1.1 1.12 79.1 0.168 6.4 4.5
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 3RCW 1.1 29.27 59008 3069 97.71 0.18173 0.18096 0.19 0.19671 0.2014 RANDOM 12.513
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] -0.25 -0.07 0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.316 r_dihedral_angle_4_deg 13.595 r_dihedral_angle_3_deg 11.019 r_dihedral_angle_1_deg 5.961 r_long_range_B_refined 4.905 r_long_range_B_other 4.408 r_scangle_other 1.938 r_angle_refined_deg 1.461 r_scbond_other 1.199 r_scbond_it 1.198
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.316 r_dihedral_angle_4_deg 13.595 r_dihedral_angle_3_deg 11.019 r_dihedral_angle_1_deg 5.961 r_long_range_B_refined 4.905 r_long_range_B_other 4.408 r_scangle_other 1.938 r_angle_refined_deg 1.461 r_scbond_other 1.199 r_scbond_it 1.198 r_mcangle_other 0.983 r_mcangle_it 0.982 r_angle_other_deg 0.95 r_mcbond_it 0.641 r_mcbond_other 0.62 r_chiral_restr 0.079 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 962 Nucleic Acid Atoms Solvent Atoms 190 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing