7BBO

Crystal Structure of the second bromodomain of Pleckstrin homology domain interacting protein (PHIP) in space group P212121


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.527720% PEG6000 -- 10% ethylene glycol -- 0.1M tris pH 7.5 -- 0.1M calcium chloride
Crystal Properties
Matthews coefficientSolvent content
2.0439.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.726α = 90
b = 56.477β = 90
c = 91.79γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2015-04-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.9173DiamondI04-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
11.3256.4899.90.99911.1659052
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.321.370.577

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE3MB31.3248.14858868284399.710.1880.18590.225521.669
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]
2.64-1.903-0.737
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg25.54
r_dihedral_angle_4_deg14.148
r_dihedral_angle_3_deg12.728
r_rigid_bond_restr6.557
r_dihedral_angle_1_deg5.592
r_lrange_it4.295
r_lrange_other4.222
r_scangle_it4.208
r_scangle_other4.207
r_scbond_it3.261
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg25.54
r_dihedral_angle_4_deg14.148
r_dihedral_angle_3_deg12.728
r_rigid_bond_restr6.557
r_dihedral_angle_1_deg5.592
r_lrange_it4.295
r_lrange_other4.222
r_scangle_it4.208
r_scangle_other4.207
r_scbond_it3.261
r_scbond_other3.261
r_mcangle_other3.018
r_mcangle_it3.015
r_mcbond_other2.354
r_mcbond_it2.347
r_angle_other_deg1.677
r_angle_refined_deg1.652
r_nbd_refined0.222
r_nbd_other0.21
r_symmetry_nbd_other0.202
r_xyhbond_nbd_refined0.188
r_nbtor_refined0.183
r_symmetry_nbd_refined0.165
r_symmetry_xyhbond_nbd_refined0.126
r_chiral_restr0.098
r_metal_ion_refined0.096
r_symmetry_nbtor_other0.076
r_bond_other_d0.014
r_bond_refined_d0.011
r_gen_planes_refined0.01
r_gen_planes_other0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2032
Nucleic Acid Atoms
Solvent Atoms196
Heterogen Atoms39

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing