5IGM

Crystal structure of the bromodomain of human BRD9 in complex with bromosporine (BSP)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52770.1 M bis tris pH 5.5, 0.2 M sodium chloride, 25% PEG3350
Crystal Properties
Matthews coefficientSolvent content
2.3146.74

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.177α = 90
b = 125.677β = 90
c = 29.787γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2013-07-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.9795DiamondI04

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
11.628.9899.90.0290.012286.43580728.4
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)
11.61.691000.5033.96.6

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 REPLACEMENTTHROUGHOUT3HME, 2GRC, 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI, 3D7C, 3DWY1.628.6933962178999.860.222480.220220.26581RANDOM38.381
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]
1.88-2.040.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.337
r_dihedral_angle_4_deg16.8
r_dihedral_angle_3_deg12.497
r_long_range_B_refined10.252
r_long_range_B_other10.25
r_scangle_other9.611
r_scbond_other7.687
r_scbond_it7.684
r_mcangle_it5.573
r_mcangle_other5.571
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.337
r_dihedral_angle_4_deg16.8
r_dihedral_angle_3_deg12.497
r_long_range_B_refined10.252
r_long_range_B_other10.25
r_scangle_other9.611
r_scbond_other7.687
r_scbond_it7.684
r_mcangle_it5.573
r_mcangle_other5.571
r_mcbond_other4.947
r_mcbond_it4.945
r_dihedral_angle_1_deg4.237
r_angle_refined_deg1.423
r_angle_other_deg0.786
r_chiral_restr0.086
r_bond_refined_d0.014
r_gen_planes_refined0.007
r_bond_other_d0.001
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 Atoms1833
Nucleic Acid Atoms
Solvent Atoms120
Heterogen Atoms44

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing