7Z9Y

BRD4 in complex with FragLite2


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
2.1242.08

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 37.967α = 90
b = 43.113β = 90
c = 79.374γ = 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
11.0439.6993.60.0660.0770.040.9969.85.759412
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)
11.041.061.2391.71.1590.3411.9

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-VALUE5LRQ1.0439.6959342293193.5740.1920.19160.20813.553
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]
0.482-0.38-0.102
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.435
r_dihedral_angle_4_deg27.359
r_dihedral_angle_3_deg11.816
r_dihedral_angle_1_deg6.002
r_lrange_it5.612
r_lrange_other5.61
r_scangle_it4.035
r_scangle_other4.033
r_scbond_it2.957
r_scbond_other2.955
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.435
r_dihedral_angle_4_deg27.359
r_dihedral_angle_3_deg11.816
r_dihedral_angle_1_deg6.002
r_lrange_it5.612
r_lrange_other5.61
r_scangle_it4.035
r_scangle_other4.033
r_scbond_it2.957
r_scbond_other2.955
r_angle_refined_deg1.89
r_mcangle_other1.869
r_mcangle_it1.853
r_angle_other_deg1.555
r_mcbond_it1.259
r_mcbond_other1.219
r_symmetry_xyhbond_nbd_refined0.366
r_nbd_refined0.263
r_nbd_other0.224
r_symmetry_nbd_refined0.214
r_xyhbond_nbd_refined0.204
r_nbtor_refined0.191
r_symmetry_nbd_other0.19
r_chiral_restr0.108
r_symmetry_xyhbond_nbd_other0.097
r_symmetry_nbtor_other0.089
r_bond_refined_d0.015
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 Atoms210
Heterogen Atoms30

Software

Software
Software NamePurpose
REFMACrefinement
REFMACrefinement
Aimlessdata scaling
xia2data reduction
PHASERphasing