6ZF9

CRYSTAL STRUCTURE OF THE FIRST BROMODOMAIN OF HUMAN BRD4 IN COMPLEX with compound SSR4


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3MXF 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP627720% w/v MMW PgSm, 100mM MES pH 6, 150 mM Ammonium nitrate, 5% ethylene glycol
Crystal Properties
Matthews coefficientSolvent content
2.1242.08

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 37.36α = 90
b = 44.13β = 90
c = 77.79γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2018-10-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.9159DiamondI04-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.277.7995.70.99921.75.139219
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.21.220.961

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 DIFFRACTIONFOURIER SYNTHESISFREE R-VALUE3MXF1.238.89539155196395.5070.1250.12350.14859.616
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]
-0.3980.655-0.256
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.473
r_dihedral_angle_3_deg10.762
r_dihedral_angle_4_deg10.331
r_dihedral_angle_1_deg6.061
r_lrange_it2.945
r_lrange_other2.939
r_scangle_it1.715
r_scangle_other1.714
r_angle_refined_deg1.61
r_angle_other_deg1.557
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.473
r_dihedral_angle_3_deg10.762
r_dihedral_angle_4_deg10.331
r_dihedral_angle_1_deg6.061
r_lrange_it2.945
r_lrange_other2.939
r_scangle_it1.715
r_scangle_other1.714
r_angle_refined_deg1.61
r_angle_other_deg1.557
r_scbond_it1.488
r_scbond_other1.487
r_rigid_bond_restr1.318
r_mcangle_other1.176
r_mcangle_it1.172
r_mcbond_it0.873
r_mcbond_other0.872
r_nbd_refined0.231
r_nbtor_refined0.19
r_nbd_other0.188
r_symmetry_nbd_other0.168
r_xyhbond_nbd_refined0.151
r_symmetry_xyhbond_nbd_refined0.123
r_symmetry_nbd_refined0.11
r_chiral_restr0.094
r_symmetry_nbtor_other0.084
r_bond_refined_d0.01
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1046
Nucleic Acid Atoms
Solvent Atoms215
Heterogen Atoms28

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
REFMACphasing