5LRQ

BRD4 in complex with ERK5 inhibitor XMD8-92


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2OSS 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7278BRD4 10mg/ml 30w/v Jeffamine ED-2001 0.1M HEPES pH7.0
Crystal Properties
Matthews coefficientSolvent content
2.2244.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.923α = 90
b = 53.923β = 90
c = 89.32γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2016-04-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.969DiamondI04-1

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
11.746.71000.081114.410.317138
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)
11.71.731000.960.912.310.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2OSS1.746.71624086299.990.18910.186670.23267RANDOM29.126
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]
-1.54-0.77-1.544.98
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.45
r_dihedral_angle_4_deg21.004
r_dihedral_angle_3_deg12.344
r_long_range_B_refined7.656
r_long_range_B_other7.641
r_dihedral_angle_1_deg7.078
r_scangle_other5.514
r_mcangle_it4.121
r_mcangle_other4.118
r_scbond_it3.47
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.45
r_dihedral_angle_4_deg21.004
r_dihedral_angle_3_deg12.344
r_long_range_B_refined7.656
r_long_range_B_other7.641
r_dihedral_angle_1_deg7.078
r_scangle_other5.514
r_mcangle_it4.121
r_mcangle_other4.118
r_scbond_it3.47
r_scbond_other3.467
r_mcbond_it2.948
r_mcbond_other2.886
r_angle_refined_deg1.888
r_angle_other_deg1.05
r_chiral_restr0.131
r_bond_refined_d0.019
r_gen_planes_refined0.013
r_bond_other_d0.004
r_gen_planes_other0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1015
Nucleic Acid Atoms
Solvent Atoms114
Heterogen Atoms35

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
PHASERphasing