5ENB

Crystal structure of the second bromodomain of Pleckstrin homology domain interacting protein (PHIP) in complex with o-Tolylthiourea (SGC - Diamond I04-1 fragment screening)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3MB3 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52770.1M HEPES pH 7.5 , 0.15M magnesium chloride , 30% PEG3350
Crystal Properties
Matthews coefficientSolvent content
2.1643.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.3α = 90
b = 92.17β = 90
c = 24.25γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2014-06-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.9200DiamondI04-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.7322.599.80.0320.0140.99925.56.414789
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.731.7899.90.7460.3070.8222.66.71045

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 REPLACEMENTTHROUGHOUT3MB31.7322.51400874199.60.2130.21180.2357RANDOM38.632
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]
-1.370.231.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.799
r_dihedral_angle_4_deg14.685
r_dihedral_angle_3_deg14.465
r_dihedral_angle_1_deg6.338
r_mcangle_it2.675
r_mcbond_it1.842
r_mcbond_other1.841
r_angle_refined_deg1.733
r_angle_other_deg1.052
r_chiral_restr0.106
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.799
r_dihedral_angle_4_deg14.685
r_dihedral_angle_3_deg14.465
r_dihedral_angle_1_deg6.338
r_mcangle_it2.675
r_mcbond_it1.842
r_mcbond_other1.841
r_angle_refined_deg1.733
r_angle_other_deg1.052
r_chiral_restr0.106
r_bond_refined_d0.016
r_gen_planes_refined0.009
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms995
Nucleic Acid Atoms
Solvent Atoms105
Heterogen Atoms19

Software

Software
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction