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BRD4 in complex with FragLite15
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 2.15 42.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.991 α = 90 b = 43.53 β = 90 c = 79.663 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 2019-09-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.911635 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 1.1 39.83 99.8 0.112 0.122 0.047 0.999 9.1 12.3 54423
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 1.1 1.12 3.468 3.884 1.722 0.315 9.7
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 1.1 39.83 54351 2636 99.728 0.21 0.2084 0.2092 0.234 0.2342 16.524
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] 0.805 -0.114 -0.691
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.966 r_dihedral_angle_4_deg 30.707 r_dihedral_angle_3_deg 11.165 r_dihedral_angle_1_deg 5.555 r_lrange_it 5.106 r_scangle_it 3.727 r_scbond_it 2.655 r_mcangle_it 1.943 r_angle_refined_deg 1.915 r_mcbond_it 1.323
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.966 r_dihedral_angle_4_deg 30.707 r_dihedral_angle_3_deg 11.165 r_dihedral_angle_1_deg 5.555 r_lrange_it 5.106 r_scangle_it 3.727 r_scbond_it 2.655 r_mcangle_it 1.943 r_angle_refined_deg 1.915 r_mcbond_it 1.323 r_xyhbond_nbd_refined 0.362 r_nbtor_refined 0.325 r_symmetry_nbd_refined 0.235 r_nbd_refined 0.217 r_symmetry_xyhbond_nbd_refined 0.194 r_chiral_restr 0.115 r_gen_planes_refined 0.014 r_bond_refined_d 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1076 Nucleic Acid Atoms Solvent Atoms 102 Heterogen Atoms 21
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Aimless data scaling xia2 data reduction PHASER phasing