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BRD4 in complex with FragLite4
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 41.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.919 α = 90 b = 43.119 β = 90 c = 79.236 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 2019-11-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.91167 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 1.12 39.62 100 0.103 0.112 0.044 0.999 12.1 12.1 50845
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 1.12 1.14 2.612 2.893 1.217 0.403 10.5
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 1.12 39.62 50776 2537 99.97 0.198 0.1963 0.1975 0.2212 0.222 15.541
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] 0.491 -0.306 -0.185
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.203 r_dihedral_angle_4_deg 32.232 r_dihedral_angle_3_deg 11.653 r_dihedral_angle_1_deg 5.825 r_lrange_it 5.611 r_scangle_it 3.649 r_scbond_it 2.582 r_mcangle_it 1.844 r_angle_refined_deg 1.814 r_mcbond_it 1.257
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.203 r_dihedral_angle_4_deg 32.232 r_dihedral_angle_3_deg 11.653 r_dihedral_angle_1_deg 5.825 r_lrange_it 5.611 r_scangle_it 3.649 r_scbond_it 2.582 r_mcangle_it 1.844 r_angle_refined_deg 1.814 r_mcbond_it 1.257 r_nbtor_refined 0.325 r_xyhbond_nbd_refined 0.262 r_symmetry_nbd_refined 0.261 r_nbd_refined 0.246 r_symmetry_xyhbond_nbd_refined 0.224 r_chiral_restr 0.102 r_gen_planes_refined 0.012 r_bond_refined_d 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1076 Nucleic Acid Atoms Solvent Atoms 174 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Aimless data scaling xia2 data reduction PHASER phasing