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BRD4 in complex with FragLite2
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 2.12 42.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.967 α = 90 b = 43.113 β = 90 c = 79.374 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 0.95397 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 1.04 39.69 93.6 0.066 0.077 0.04 0.996 9.8 5.7 59412
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 1.04 1.06 1.239 1.7 1.159 0.341 1.9
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 1.04 39.69 59342 2931 93.574 0.192 0.1916 0.1918 0.208 0.2082 13.553
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] 0.482 -0.38 -0.102
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.435 r_dihedral_angle_4_deg 27.359 r_dihedral_angle_3_deg 11.816 r_dihedral_angle_1_deg 6.002 r_lrange_it 5.612 r_lrange_other 5.61 r_scangle_it 4.035 r_scangle_other 4.033 r_scbond_it 2.957 r_scbond_other 2.955
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.435 r_dihedral_angle_4_deg 27.359 r_dihedral_angle_3_deg 11.816 r_dihedral_angle_1_deg 6.002 r_lrange_it 5.612 r_lrange_other 5.61 r_scangle_it 4.035 r_scangle_other 4.033 r_scbond_it 2.957 r_scbond_other 2.955 r_angle_refined_deg 1.89 r_mcangle_other 1.869 r_mcangle_it 1.853 r_angle_other_deg 1.555 r_mcbond_it 1.259 r_mcbond_other 1.219 r_symmetry_xyhbond_nbd_refined 0.366 r_nbd_refined 0.263 r_nbd_other 0.224 r_symmetry_nbd_refined 0.214 r_xyhbond_nbd_refined 0.204 r_nbtor_refined 0.191 r_symmetry_nbd_other 0.19 r_chiral_restr 0.108 r_symmetry_xyhbond_nbd_other 0.097 r_symmetry_nbtor_other 0.089 r_bond_refined_d 0.015 r_gen_planes_refined 0.011 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1076 Nucleic Acid Atoms Solvent Atoms 210 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Aimless data scaling xia2 data reduction PHASER phasing