7ZAD

BRD4 in complex with FragLite12


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
2.1141.79

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 37.898α = 90
b = 43.111β = 90
c = 79.12γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2019-09-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.911628DiamondI04-1

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
11.0739.5698.50.0630.0680.026114.612.857056
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)
11.071.093.1453.5621.6210.38.2

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-VALUE5LRQ1.0739.5656992280298.2590.2040.20280.2317.74
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]
0.9-0.861-0.039
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.381
r_dihedral_angle_4_deg26.659
r_dihedral_angle_3_deg12.518
r_dihedral_angle_1_deg6.449
r_lrange_it6.148
r_scangle_it5.016
r_scbond_it4.617
r_mcangle_it1.999
r_angle_refined_deg1.951
r_mcbond_it1.386
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.381
r_dihedral_angle_4_deg26.659
r_dihedral_angle_3_deg12.518
r_dihedral_angle_1_deg6.449
r_lrange_it6.148
r_scangle_it5.016
r_scbond_it4.617
r_mcangle_it1.999
r_angle_refined_deg1.951
r_mcbond_it1.386
r_nbtor_refined0.325
r_xyhbond_nbd_refined0.252
r_nbd_refined0.24
r_symmetry_nbd_refined0.215
r_symmetry_xyhbond_nbd_refined0.21
r_chiral_restr0.109
r_bond_refined_d0.013
r_gen_planes_refined0.013
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1076
Nucleic Acid Atoms
Solvent Atoms177
Heterogen Atoms22

Software

Software
Software NamePurpose
REFMACrefinement
REFMACrefinement
Aimlessdata scaling
xia2data reduction
PHASERphasing