5S8O

XChem group deposition -- Crystal Structure of the second bromodomain of pleckstrin homology domain interacting protein (PHIP) in complex with N01460c (space group P212121)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52770.1M HEPES pH 7.5 -- 0.1M calcium chloride -- 10% ethylene glycol -- 17% PEG6K
Crystal Properties
Matthews coefficientSolvent content
2.0439.83

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.57α = 90
b = 57.17β = 90
c = 91.14γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2017-10-03SINGLE 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)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
11.6745.5799.90.0750.080.030.99914.87.229591
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)
11.671.7199.91.591.7150.6360.55672165

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT3MB31.6745.5728057148099.840.21710.21550.2454RANDOM26.384
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]
0.87-0.8-0.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg24.532
r_dihedral_angle_3_deg14.36
r_dihedral_angle_4_deg11.259
r_dihedral_angle_1_deg5.595
r_mcangle_it2.713
r_mcbond_it1.853
r_mcbond_other1.844
r_angle_refined_deg1.377
r_angle_other_deg1.366
r_chiral_restr0.074
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg24.532
r_dihedral_angle_3_deg14.36
r_dihedral_angle_4_deg11.259
r_dihedral_angle_1_deg5.595
r_mcangle_it2.713
r_mcbond_it1.853
r_mcbond_other1.844
r_angle_refined_deg1.377
r_angle_other_deg1.366
r_chiral_restr0.074
r_bond_refined_d0.007
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1973
Nucleic Acid Atoms
Solvent Atoms166
Heterogen Atoms38

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing