7ZFS

BRD4 in complex with FragLite32


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
2.1141.65

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 37.842α = 90
b = 43.142β = 90
c = 78.99γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2019-09-25MSINGLE 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
11.2539.491000.1070.1160.0430.99910.613.236606
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)
11.251.274.2934.6651.8150.32312.5

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-VALUE5LRQ1.2539.4936539189599.940.2040.20250.226920.235
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]
0.891-0.481-0.41
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.715
r_dihedral_angle_4_deg31.046
r_dihedral_angle_3_deg12.904
r_dihedral_angle_1_deg5.644
r_lrange_it5.624
r_scangle_it4.031
r_scbond_it2.952
r_mcangle_it2.164
r_angle_refined_deg1.845
r_mcbond_it1.498
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.715
r_dihedral_angle_4_deg31.046
r_dihedral_angle_3_deg12.904
r_dihedral_angle_1_deg5.644
r_lrange_it5.624
r_scangle_it4.031
r_scbond_it2.952
r_mcangle_it2.164
r_angle_refined_deg1.845
r_mcbond_it1.498
r_nbtor_refined0.327
r_nbd_refined0.229
r_symmetry_xyhbond_nbd_refined0.224
r_symmetry_nbd_refined0.203
r_xyhbond_nbd_refined0.147
r_chiral_restr0.113
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 Atoms155
Heterogen Atoms21

Software

Software
Software NamePurpose
REFMACrefinement
REFMACrefinement
Aimlessdata scaling
xia2data reduction
PHASERphasing