7ZA6

BRD4 in complex with FragLite4


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
2.1241.92

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 37.919α = 90
b = 43.119β = 90
c = 79.236γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2019-11-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.91167DiamondI04-1

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
11.1239.621000.1030.1120.0440.99912.112.150845
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)
11.121.142.6122.8931.2170.40310.5

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-VALUE5LRQ1.1239.6250776253799.970.1980.19630.221215.541
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
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.203
r_dihedral_angle_4_deg32.232
r_dihedral_angle_3_deg11.653
r_dihedral_angle_1_deg5.825
r_lrange_it5.611
r_scangle_it3.649
r_scbond_it2.582
r_mcangle_it1.844
r_angle_refined_deg1.814
r_mcbond_it1.257
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.203
r_dihedral_angle_4_deg32.232
r_dihedral_angle_3_deg11.653
r_dihedral_angle_1_deg5.825
r_lrange_it5.611
r_scangle_it3.649
r_scbond_it2.582
r_mcangle_it1.844
r_angle_refined_deg1.814
r_mcbond_it1.257
r_nbtor_refined0.325
r_xyhbond_nbd_refined0.262
r_symmetry_nbd_refined0.261
r_nbd_refined0.246
r_symmetry_xyhbond_nbd_refined0.224
r_chiral_restr0.102
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 Atoms174
Heterogen Atoms26

Software

Software
Software NamePurpose
REFMACrefinement
REFMACrefinement
Aimlessdata scaling
xia2data reduction
PHASERphasing