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BRD4 in complex with FragLite19
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5LRQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 0.1 M Buffer system 3 (1 M Tris, 1 M BICINE, pH 8.5), 34-44% Precipitant Solution 3 (20% PEG 4000, 40%) and 60-80 mM Halogens Mix (NaF, NaBr and NaI) solution
Crystal Properties Matthews coefficient Solvent content 2.14 42.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.732 α = 90 b = 43.555 β = 90 c = 79.628 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 2019-08-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.953970 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.11 39.81 99.3 0.072 0.084 0.044 0.997 8.4 6.1 52376
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.11 1.13 1.398 1.843 1.187 0.315 2.9
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5LRQ 1.11 39.81 52306 2603 99.318 0.194 0.1934 0.1936 0.214 0.214 15.551
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] 0.56 -0.191 -0.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.688 r_lrange_it 6.347 r_lrange_other 6.345 r_scangle_it 4.542 r_scangle_other 4.54 r_dihedral_angle_2_deg 3.979 r_scbond_it 3.149 r_scbond_other 3.147 r_mcangle_other 2.014 r_mcangle_it 2.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.688 r_lrange_it 6.347 r_lrange_other 6.345 r_scangle_it 4.542 r_scangle_other 4.54 r_dihedral_angle_2_deg 3.979 r_scbond_it 3.149 r_scbond_other 3.147 r_mcangle_other 2.014 r_mcangle_it 2.003 r_angle_refined_deg 1.762 r_mcbond_it 1.361 r_mcbond_other 1.329 r_angle_other_deg 0.567 r_nbd_refined 0.272 r_xyhbond_nbd_refined 0.241 r_nbtor_refined 0.196 r_symmetry_nbd_other 0.19 r_nbd_other 0.187 r_symmetry_xyhbond_nbd_refined 0.18 r_symmetry_nbd_refined 0.154 r_chiral_restr 0.093 r_symmetry_nbtor_other 0.079 r_bond_refined_d 0.011 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1076 Nucleic Acid Atoms Solvent Atoms 118 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Aimless data scaling xia2 data reduction PHASER phasing