7ZFZ

BRD4 in complex with PepLite-Val


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
2.1342.24

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 37.808α = 90
b = 43.417β = 90
c = 79.36γ = 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 I04-10.953970DiamondI04-1

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
11.0839.6895.50.0730.0860.0450.99886.154177
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)
11.081.11.4131.8211.1360.3273.1

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-VALUE5LRQ1.0839.6854111265595.1820.2070.20560.236417.505
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]
0.381-0.298-0.083
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.326
r_dihedral_angle_4_deg26.845
r_dihedral_angle_3_deg12.55
r_lrange_it6.935
r_dihedral_angle_1_deg6.234
r_scangle_it4.826
r_scbond_it3.643
r_angle_refined_deg2.078
r_mcangle_it1.988
r_mcbond_it1.335
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.326
r_dihedral_angle_4_deg26.845
r_dihedral_angle_3_deg12.55
r_lrange_it6.935
r_dihedral_angle_1_deg6.234
r_scangle_it4.826
r_scbond_it3.643
r_angle_refined_deg2.078
r_mcangle_it1.988
r_mcbond_it1.335
r_nbtor_refined0.324
r_nbd_refined0.245
r_symmetry_nbd_refined0.211
r_xyhbond_nbd_refined0.182
r_symmetry_xyhbond_nbd_refined0.168
r_chiral_restr0.115
r_bond_refined_d0.014
r_gen_planes_refined0.011
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1076
Nucleic Acid Atoms
Solvent Atoms145
Heterogen Atoms27

Software

Software
Software NamePurpose
REFMACrefinement
REFMACrefinement
Aimlessdata scaling
xia2data reduction
PHASERphasing