5S8D

XChem group deposition -- Crystal Structure of the second bromodomain of pleckstrin homology domain interacting protein (PHIP) in complex with N00539e (space group C2)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP52770.04M potassium phosphate monobasic -- 11% PEG8K
Crystal Properties
Matthews coefficientSolvent content
2.141.32

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.85α = 90
b = 27.52β = 100.25
c = 56.64γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2016-06-23SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.92819DiamondI04-1

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
11.2640.7696.20.0340.0420.0230.99916.82.833081
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)
11.261.2992.90.7891.0390.6690.53922342

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 SYNTHESISTHROUGHOUT7AV91.2640.7631439163896.140.17670.17490.2084RANDOM18.052
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]
0.851.54-0.43-0.91
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg24.661
r_dihedral_angle_4_deg14.156
r_dihedral_angle_3_deg11.788
r_dihedral_angle_1_deg5.306
r_rigid_bond_restr3.141
r_mcangle_it2.223
r_mcbond_it2.026
r_mcbond_other1.962
r_angle_refined_deg1.779
r_angle_other_deg1.557
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg24.661
r_dihedral_angle_4_deg14.156
r_dihedral_angle_3_deg11.788
r_dihedral_angle_1_deg5.306
r_rigid_bond_restr3.141
r_mcangle_it2.223
r_mcbond_it2.026
r_mcbond_other1.962
r_angle_refined_deg1.779
r_angle_other_deg1.557
r_chiral_restr0.11
r_bond_refined_d0.012
r_gen_planes_refined0.01
r_bond_other_d0.005
r_gen_planes_other0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms990
Nucleic Acid Atoms
Solvent Atoms116
Heterogen Atoms14

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing