7ZA7

BRD4 in complex with FragLite5


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
2.1241.99

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 38.013α = 90
b = 43.068β = 90
c = 79.228γ = 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 I04-10.95397DiamondI04-1

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
11.0639.6193.30.0770.0890.0450.99312.5655793
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)
11.061.081.752.1991.3010.342.7

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-VALUE5LRQ1.0639.6155724274893.1780.1960.19540.206213.093
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]
0.523-0.6090.086
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.409
r_dihedral_angle_4_deg32.141
r_dihedral_angle_3_deg12.126
r_lrange_it6.648
r_lrange_other6.646
r_dihedral_angle_1_deg6.472
r_scangle_it4.17
r_scangle_other4.168
r_scbond_it3.042
r_scbond_other3.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.409
r_dihedral_angle_4_deg32.141
r_dihedral_angle_3_deg12.126
r_lrange_it6.648
r_lrange_other6.646
r_dihedral_angle_1_deg6.472
r_scangle_it4.17
r_scangle_other4.168
r_scbond_it3.042
r_scbond_other3.04
r_angle_refined_deg1.914
r_mcangle_other1.828
r_mcangle_it1.817
r_angle_other_deg1.588
r_mcbond_it1.215
r_mcbond_other1.185
r_symmetry_xyhbond_nbd_refined0.326
r_xyhbond_nbd_refined0.26
r_nbd_refined0.247
r_nbd_other0.224
r_symmetry_nbd_refined0.218
r_nbtor_refined0.196
r_symmetry_nbd_other0.182
r_chiral_restr0.115
r_symmetry_nbtor_other0.088
r_bond_refined_d0.016
r_gen_planes_refined0.011
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1076
Nucleic Acid Atoms
Solvent Atoms163
Heterogen Atoms28

Software

Software
Software NamePurpose
REFMACrefinement
REFMACrefinement
Aimlessdata scaling
xia2data reduction
PHASERphasing