4Z6I

Crystal structure of BRD9 bromodomain in complex with a substituted valerolactam quinolone ligand


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6277.150.1M MMT pH6, 30% PEG 1k
Crystal Properties
Matthews coefficientSolvent content
2.1943.91

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.015α = 90
b = 29.458β = 92.24
c = 141.187γ = 90
Symmetry
Space GroupI 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2013-09-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I240.9795DiamondI24

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
11.9528.8498.30.0330.03220.33.21812718127
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)
11.95297.90.1236.13

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 REPLACEMENTTHROUGHOUT3HME1.9528.841712192397.670.183720.181180.22989RANDOM30.104
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]
-0.80.72.26-1.51
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.006
r_dihedral_angle_3_deg14.371
r_dihedral_angle_4_deg12.165
r_dihedral_angle_1_deg5.68
r_long_range_B_refined5.486
r_long_range_B_other5.443
r_scangle_other4.094
r_scbond_it2.632
r_scbond_other2.631
r_mcangle_it2.293
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.006
r_dihedral_angle_3_deg14.371
r_dihedral_angle_4_deg12.165
r_dihedral_angle_1_deg5.68
r_long_range_B_refined5.486
r_long_range_B_other5.443
r_scangle_other4.094
r_scbond_it2.632
r_scbond_other2.631
r_mcangle_it2.293
r_mcangle_other2.293
r_angle_refined_deg2.069
r_mcbond_it1.681
r_mcbond_other1.675
r_angle_other_deg1.125
r_chiral_restr0.139
r_bond_refined_d0.021
r_gen_planes_refined0.012
r_bond_other_d0.002
r_gen_planes_other0.001
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 Atoms1840
Nucleic Acid Atoms
Solvent Atoms111
Heterogen Atoms68

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing