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N-TERMINAL BROMODOMAIN OF HUMAN BRD4 WITH compound 5ef
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other in house model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 0.1 sodium citrate pH 5.6, 10% w/v PEG4K, 10% w/v propan-2-ol
Crystal Properties Matthews coefficient Solvent content 2.18 43.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.035 α = 90 b = 52.166 β = 90.144 c = 59.957 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 PILATUS 6M 2017-08-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.97951 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.88 59.96 96.3 0.043 0.999 16.8 3.4 20355
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.88 1.92 96.3 0.478 0.839 2.4 3.3
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 (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE in house model 1.881 59.957 20354 1071 95.775 0.179 0.177 0.222 0.2427 34.513
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] -15.037 -4.747 7.438 7.599
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.818 r_dihedral_angle_4_deg 13.478 r_dihedral_angle_3_deg 13.277 r_lrange_it 7.274 r_lrange_other 7.273 r_dihedral_angle_1_deg 5.809 r_scangle_it 4.798 r_scangle_other 4.797 r_mcangle_it 3.771 r_mcangle_other 3.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.818 r_dihedral_angle_4_deg 13.478 r_dihedral_angle_3_deg 13.277 r_lrange_it 7.274 r_lrange_other 7.273 r_dihedral_angle_1_deg 5.809 r_scangle_it 4.798 r_scangle_other 4.797 r_mcangle_it 3.771 r_mcangle_other 3.77 r_scbond_it 3.133 r_scbond_other 3.132 r_mcbond_it 2.675 r_mcbond_other 2.659 r_angle_refined_deg 1.308 r_angle_other_deg 1.133 r_symmetry_nbd_refined 0.207 r_nbd_refined 0.193 r_nbd_other 0.185 r_symmetry_nbd_other 0.176 r_xyhbond_nbd_refined 0.172 r_nbtor_refined 0.17 r_symmetry_xyhbond_nbd_refined 0.154 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.058 r_bond_refined_d 0.005 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 2096 Nucleic Acid Atoms Solvent Atoms 208 Heterogen Atoms 130
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling