7S4E

Crystal Structure of ligand ACBi1 in complex with bromodomain of human Smarca2 and pVHL:ElonginC:ElonginB complex


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6HAX 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.85277.150.1 M HEPES, pH 7.85, 13% PEG 3350, 0.2 M sodium formate
Crystal Properties
Matthews coefficientSolvent content
2.6854.05

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.14α = 90
b = 116.57β = 90
c = 122.32γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray77.15PIXELDECTRIS EIGER X 16M2021-06-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS-II BEAMLINE 17-ID-20.97932NSLS-II17-ID-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
12.2537.9299.90.1490.160.0580.99887.455100
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.252.3199.92.6022.7971.0170.3177.4

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 REPLACEMENTFREE R-VALUE6HAX2.2537.9252206282899.920.2210.2190.2587RANDOM61.139
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]
-3.16-0.213.37
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.404
r_dihedral_angle_4_deg20.826
r_dihedral_angle_3_deg15.636
r_dihedral_angle_1_deg7.601
r_angle_refined_deg1.519
r_angle_other_deg1.185
r_chiral_restr0.065
r_bond_refined_d0.009
r_gen_planes_refined0.007
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.404
r_dihedral_angle_4_deg20.826
r_dihedral_angle_3_deg15.636
r_dihedral_angle_1_deg7.601
r_angle_refined_deg1.519
r_angle_other_deg1.185
r_chiral_restr0.065
r_bond_refined_d0.009
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7356
Nucleic Acid Atoms
Solvent Atoms90
Heterogen Atoms196

Software

Software
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Cootmodel building
PHASERphasing