7ZEN

BRD4 in complex with FragLite23


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
2.1342.25

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 38.005α = 90
b = 43.206β = 90
c = 79.348γ = 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 I04-10.953970DiamondI04-1

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
11.1439.6799.80.080.0940.0490.9989.86.448392
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)
11.141.161.2871.651.0150.3294

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-VALUE5LRQ1.1439.6748325235599.6950.1970.19640.209814.593
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]
0.406-0.4290.023
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.348
r_dihedral_angle_4_deg34.482
r_dihedral_angle_3_deg11.683
r_dihedral_angle_1_deg5.986
r_lrange_it5.133
r_scangle_it3.888
r_scbond_it2.769
r_angle_refined_deg1.972
r_mcangle_it1.906
r_mcbond_it1.286
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.348
r_dihedral_angle_4_deg34.482
r_dihedral_angle_3_deg11.683
r_dihedral_angle_1_deg5.986
r_lrange_it5.133
r_scangle_it3.888
r_scbond_it2.769
r_angle_refined_deg1.972
r_mcangle_it1.906
r_mcbond_it1.286
r_nbtor_refined0.328
r_symmetry_xyhbond_nbd_refined0.27
r_nbd_refined0.232
r_xyhbond_nbd_refined0.201
r_symmetry_nbd_refined0.196
r_chiral_restr0.1
r_bond_refined_d0.012
r_gen_planes_refined0.012
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1076
Nucleic Acid Atoms
Solvent Atoms148
Heterogen Atoms21

Software

Software
Software NamePurpose
REFMACrefinement
REFMACrefinement
Aimlessdata scaling
xia2data reduction
PHASERphasing