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BRD4 in complex with FragLite5
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 41.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.013 α = 90 b = 43.068 β = 90 c = 79.228 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 1.06 39.61 93.3 0.077 0.089 0.045 0.993 12.5 6 55793
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 1.06 1.08 1.75 2.199 1.301 0.34 2.7
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 1.06 39.61 55724 2748 93.178 0.196 0.1954 0.1957 0.2062 0.2066 13.093
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] 0.523 -0.609 0.086
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.409 r_dihedral_angle_4_deg 32.141 r_dihedral_angle_3_deg 12.126 r_lrange_it 6.648 r_lrange_other 6.646 r_dihedral_angle_1_deg 6.472 r_scangle_it 4.17 r_scangle_other 4.168 r_scbond_it 3.042 r_scbond_other 3.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.409 r_dihedral_angle_4_deg 32.141 r_dihedral_angle_3_deg 12.126 r_lrange_it 6.648 r_lrange_other 6.646 r_dihedral_angle_1_deg 6.472 r_scangle_it 4.17 r_scangle_other 4.168 r_scbond_it 3.042 r_scbond_other 3.04 r_angle_refined_deg 1.914 r_mcangle_other 1.828 r_mcangle_it 1.817 r_angle_other_deg 1.588 r_mcbond_it 1.215 r_mcbond_other 1.185 r_symmetry_xyhbond_nbd_refined 0.326 r_xyhbond_nbd_refined 0.26 r_nbd_refined 0.247 r_nbd_other 0.224 r_symmetry_nbd_refined 0.218 r_nbtor_refined 0.196 r_symmetry_nbd_other 0.182 r_chiral_restr 0.115 r_symmetry_nbtor_other 0.088 r_bond_refined_d 0.016 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 163 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Aimless data scaling xia2 data reduction PHASER phasing