7ZFY

BRD4 in complex with PepLite-Gly


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
2.1642.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 37.896α = 90
b = 43.531β = 90
c = 79.967γ = 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 I04-10.911635DiamondI04-1

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
11.1539.981000.1010.110.042111.812.947837
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)
11.151.173.2993.5781.3740.37113

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-VALUE5LRQ1.1539.9847768233399.9670.1980.19690.213318.007
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]
0.595-0.548-0.048
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.696
r_dihedral_angle_4_deg27.74
r_dihedral_angle_3_deg12.73
r_lrange_it6.94
r_dihedral_angle_1_deg5.505
r_scangle_it4.402
r_scbond_it3.398
r_angle_refined_deg1.969
r_mcangle_it1.905
r_mcbond_it1.272
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.696
r_dihedral_angle_4_deg27.74
r_dihedral_angle_3_deg12.73
r_lrange_it6.94
r_dihedral_angle_1_deg5.505
r_scangle_it4.402
r_scbond_it3.398
r_angle_refined_deg1.969
r_mcangle_it1.905
r_mcbond_it1.272
r_symmetry_nbd_refined0.357
r_nbtor_refined0.321
r_xyhbond_nbd_refined0.277
r_nbd_refined0.238
r_symmetry_xyhbond_nbd_refined0.219
r_chiral_restr0.119
r_bond_refined_d0.015
r_gen_planes_refined0.011
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1076
Nucleic Acid Atoms
Solvent Atoms122
Heterogen Atoms60

Software

Software
Software NamePurpose
REFMACrefinement
REFMACrefinement
Aimlessdata scaling
xia2data reduction
PHASERphasing