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BRD4 in complex with FragLite24
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 2.1 41.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.793 α = 90 b = 43.134 β = 90 c = 78.998 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 0.911635 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 1.12 39.5 100 0.103 0.112 0.043 0.999 11.2 13.1 50545
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 6.039 6.649 2.759 0.439 11.2
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 39.5 50474 2526 99.958 0.212 0.2107 0.211 0.2436 0.244 19.312
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] 1.521 -1.091 -0.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.168 r_dihedral_angle_4_deg 28.796 r_dihedral_angle_3_deg 12.846 r_lrange_it 7.301 r_dihedral_angle_1_deg 6.823 r_scangle_it 4.197 r_scbond_it 3.009 r_mcangle_it 2.14 r_angle_refined_deg 1.937 r_mcbond_it 1.458
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.168 r_dihedral_angle_4_deg 28.796 r_dihedral_angle_3_deg 12.846 r_lrange_it 7.301 r_dihedral_angle_1_deg 6.823 r_scangle_it 4.197 r_scbond_it 3.009 r_mcangle_it 2.14 r_angle_refined_deg 1.937 r_mcbond_it 1.458 r_nbtor_refined 0.325 r_nbd_refined 0.231 r_symmetry_xyhbond_nbd_refined 0.217 r_xyhbond_nbd_refined 0.212 r_symmetry_nbd_refined 0.201 r_chiral_restr 0.149 r_gen_planes_refined 0.013 r_bond_refined_d 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1076 Nucleic Acid Atoms Solvent Atoms 159 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Aimless data scaling xia2 data reduction PHASER phasing