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Crystal structure of the bromodomain of human Bromodomain and PHD finger-containing Transcription Factor (BPTF) bound to a potent inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7K6R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 0.20M KSCN; 0.1M BTProp pH 6.5; 20.0% PEG 3350; 10.0% EtGly
Crystal Properties Matthews coefficient Solvent content 2.11 41.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.277 α = 90 b = 27.043 β = 93.48 c = 77.637 γ = 90
Symmetry Space Group P 1 21 1
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 EIGER2 XE 16M 2022-10-18 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) CC (Half) 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 1.6 77.494 95.5 0.998 10.8 3.5 200470
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.601 1.648 0.743
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.6 77.49 27919 1540 90.51 0.18268 0.18052 0.22243 0.2237 RANDOM 12.398
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] -0.1 -0.02 0.02 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.489 r_dihedral_angle_4_deg 19.118 r_dihedral_angle_3_deg 11.771 r_dihedral_angle_1_deg 5.453 r_long_range_B_refined 4.424 r_long_range_B_other 4.424 r_scangle_other 2.527 r_scbond_it 1.702 r_scbond_other 1.702 r_angle_refined_deg 1.608
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.489 r_dihedral_angle_4_deg 19.118 r_dihedral_angle_3_deg 11.771 r_dihedral_angle_1_deg 5.453 r_long_range_B_refined 4.424 r_long_range_B_other 4.424 r_scangle_other 2.527 r_scbond_it 1.702 r_scbond_other 1.702 r_angle_refined_deg 1.608 r_angle_other_deg 1.429 r_mcangle_other 1.352 r_mcangle_it 1.351 r_mcbond_it 0.94 r_mcbond_other 0.907 r_chiral_restr 0.08 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 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 1988 Nucleic Acid Atoms Solvent Atoms 354 Heterogen Atoms 112
Software Software Software Name Purpose REFMAC refinement XDS data reduction STARANISO data scaling MOLREP phasing