7ZAQ

BRD4 in complex with FragLite19


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5LRQ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52930.1 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 coefficientSolvent content
2.1442.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 37.732α = 90
b = 43.555β = 90
c = 79.628γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2019-08-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.953970DiamondI04-1

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.1139.8199.30.0720.0840.0440.9978.46.152376
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)RedundancyNumber Unique Reflections (All)
11.111.131.3981.8431.1870.3152.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE5LRQ1.1139.8152306260399.3180.1940.19340.21415.551
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]
0.56-0.191-0.37
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.688
r_lrange_it6.347
r_lrange_other6.345
r_scangle_it4.542
r_scangle_other4.54
r_dihedral_angle_2_deg3.979
r_scbond_it3.149
r_scbond_other3.147
r_mcangle_other2.014
r_mcangle_it2.003
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.688
r_lrange_it6.347
r_lrange_other6.345
r_scangle_it4.542
r_scangle_other4.54
r_dihedral_angle_2_deg3.979
r_scbond_it3.149
r_scbond_other3.147
r_mcangle_other2.014
r_mcangle_it2.003
r_angle_refined_deg1.762
r_mcbond_it1.361
r_mcbond_other1.329
r_angle_other_deg0.567
r_nbd_refined0.272
r_xyhbond_nbd_refined0.241
r_nbtor_refined0.196
r_symmetry_nbd_other0.19
r_nbd_other0.187
r_symmetry_xyhbond_nbd_refined0.18
r_symmetry_nbd_refined0.154
r_chiral_restr0.093
r_symmetry_nbtor_other0.079
r_bond_refined_d0.011
r_gen_planes_refined0.011
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1076
Nucleic Acid Atoms
Solvent Atoms118
Heterogen Atoms28

Software

Software
Software NamePurpose
REFMACrefinement
REFMACrefinement
Aimlessdata scaling
xia2data reduction
PHASERphasing