7ZA9

BRD4 in complex with FragLite7


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
2.1342.17

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 37.83α = 90
b = 43.374β = 90
c = 79.299γ = 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 I04-10.95397DiamondI04-1

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
11.0539.6587.90.0470.0550.0290.99913.96.354042
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)
11.051.071.191.5410.9670.3143.2

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-VALUE5LRQ1.0539.6553987266187.4950.2060.20530.223514.939
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]
0.465-0.5650.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.165
r_dihedral_angle_4_deg23.753
r_dihedral_angle_3_deg12.138
r_dihedral_angle_1_deg5.656
r_lrange_it5.13
r_scangle_it3.693
r_scbond_it2.699
r_angle_refined_deg1.891
r_mcangle_it1.789
r_mcbond_it1.263
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.165
r_dihedral_angle_4_deg23.753
r_dihedral_angle_3_deg12.138
r_dihedral_angle_1_deg5.656
r_lrange_it5.13
r_scangle_it3.693
r_scbond_it2.699
r_angle_refined_deg1.891
r_mcangle_it1.789
r_mcbond_it1.263
r_nbtor_refined0.325
r_symmetry_xyhbond_nbd_refined0.253
r_nbd_refined0.234
r_symmetry_nbd_refined0.223
r_xyhbond_nbd_refined0.194
r_chiral_restr0.132
r_gen_planes_refined0.012
r_bond_refined_d0.011
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1076
Nucleic Acid Atoms
Solvent Atoms117
Heterogen Atoms38

Software

Software
Software NamePurpose
REFMACrefinement
REFMACrefinement
Aimlessdata scaling
xia2data reduction
PHASERphasing