5DKD

Crystal structure of the bromodomain of human BRG1 (SMARCA4) in complex with PFI-3 chemical probe


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.2277.150.1 M Bis Tris pH 7.2, 0.1 M ammonium acetate, 0.1 M ZnCl2, 15% PEG smear high (mixture from PEG8k to 20k)
Crystal Properties
Matthews coefficientSolvent content
2.9858.78

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.926α = 90
b = 74.566β = 109.9
c = 52.626γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2014-04-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.9207DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)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
1229.7896.80.0760.0549.83.521859
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.0595.70.3043.33.6

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 REPLACEMENTTHROUGHOUT3UVD229.7820159102793.850.26920.267730.29729RANDOM32.2
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]
2.120.16-1.2-0.82
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.766
r_dihedral_angle_3_deg16.667
r_dihedral_angle_4_deg15.155
r_dihedral_angle_1_deg6.168
r_long_range_B_refined5.897
r_long_range_B_other5.86
r_scangle_other4.26
r_mcangle_it2.708
r_mcangle_other2.707
r_scbond_it2.647
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.766
r_dihedral_angle_3_deg16.667
r_dihedral_angle_4_deg15.155
r_dihedral_angle_1_deg6.168
r_long_range_B_refined5.897
r_long_range_B_other5.86
r_scangle_other4.26
r_mcangle_it2.708
r_mcangle_other2.707
r_scbond_it2.647
r_scbond_other2.647
r_mcbond_it1.773
r_mcbond_other1.771
r_angle_refined_deg1.741
r_angle_other_deg1.246
r_chiral_restr0.107
r_bond_refined_d0.015
r_gen_planes_refined0.009
r_bond_other_d0.004
r_gen_planes_other0.003
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 Atoms1827
Nucleic Acid Atoms
Solvent Atoms101
Heterogen Atoms74

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing