7ZFN

BRD4 in complex with FragLite24


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
2.141.57

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 37.793α = 90
b = 43.134β = 90
c = 78.998γ = 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
11.1239.51000.1030.1120.0430.99911.213.150545
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)
11.121.146.0396.6492.7590.43911.2

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-VALUE5LRQ1.1239.550474252699.9580.2120.21070.243619.312
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]
1.521-1.091-0.43
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.168
r_dihedral_angle_4_deg28.796
r_dihedral_angle_3_deg12.846
r_lrange_it7.301
r_dihedral_angle_1_deg6.823
r_scangle_it4.197
r_scbond_it3.009
r_mcangle_it2.14
r_angle_refined_deg1.937
r_mcbond_it1.458
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.168
r_dihedral_angle_4_deg28.796
r_dihedral_angle_3_deg12.846
r_lrange_it7.301
r_dihedral_angle_1_deg6.823
r_scangle_it4.197
r_scbond_it3.009
r_mcangle_it2.14
r_angle_refined_deg1.937
r_mcbond_it1.458
r_nbtor_refined0.325
r_nbd_refined0.231
r_symmetry_xyhbond_nbd_refined0.217
r_xyhbond_nbd_refined0.212
r_symmetry_nbd_refined0.201
r_chiral_restr0.149
r_gen_planes_refined0.013
r_bond_refined_d0.011
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1076
Nucleic Acid Atoms
Solvent Atoms159
Heterogen Atoms28

Software

Software
Software NamePurpose
REFMACrefinement
REFMACrefinement
Aimlessdata scaling
xia2data reduction
PHASERphasing