7Z9W

BRD4 in complex with FragLite1


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 = 38.008α = 90
b = 43.052β = 90
c = 79.399γ = 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)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
10.98839.73183.60.0450.99812.75.561691
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
10.9881.017.60.750.4041.1

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-VALUE5LRQ0.98839.73161616310183.5690.2010.19940.220515.901
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]
0.534-0.457-0.078
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.523
r_dihedral_angle_4_deg31.793
r_dihedral_angle_3_deg12.012
r_dihedral_angle_1_deg5.682
r_lrange_it5.215
r_scangle_it3.612
r_scbond_it2.517
r_mcangle_it1.912
r_angle_refined_deg1.823
r_mcbond_it1.353
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.523
r_dihedral_angle_4_deg31.793
r_dihedral_angle_3_deg12.012
r_dihedral_angle_1_deg5.682
r_lrange_it5.215
r_scangle_it3.612
r_scbond_it2.517
r_mcangle_it1.912
r_angle_refined_deg1.823
r_mcbond_it1.353
r_symmetry_xyhbond_nbd_refined0.429
r_nbtor_refined0.322
r_nbd_refined0.254
r_symmetry_nbd_refined0.222
r_xyhbond_nbd_refined0.202
r_chiral_restr0.098
r_gen_planes_refined0.012
r_bond_refined_d0.011
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1076
Nucleic Acid Atoms
Solvent Atoms174
Heterogen Atoms18

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
PHASERphasing