5FE6

Crystal structure of human PCAF bromodomain in complex with fragment ZB1916 (fragment 10)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3GG3pdb id 3GG3

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP277.1521-35% PEG 3350, 0.1 M Bis-Tris pH 5.5-7.0 or 21-40% medium-molecular-weight PEG smears (MMW PEG smears) buffered either with 0.1 M Bis-Tris pH 6.0-7.5 or 0.1 M Tris pH 7.5-8.8
Crystal Properties
Matthews coefficientSolvent content
3.3863.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 99.939α = 90
b = 99.939β = 90
c = 99.672γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2014-05-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.97625DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.7719.8599.90.0516.55.13618836.7
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.771.8799.90.6092.24.3

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 REPLACEMENTTHROUGHOUTpdb id 3GG31.7719.8534410177899.90.181030.179410.21248RANDOM45.06
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]
-0.06-0.03-0.060.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.92
r_dihedral_angle_4_deg22.859
r_dihedral_angle_3_deg12.043
r_long_range_B_refined8.684
r_long_range_B_other8.683
r_dihedral_angle_1_deg5.392
r_scangle_other5.263
r_scbond_it3.761
r_scbond_other3.76
r_mcangle_it3.342
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.92
r_dihedral_angle_4_deg22.859
r_dihedral_angle_3_deg12.043
r_long_range_B_refined8.684
r_long_range_B_other8.683
r_dihedral_angle_1_deg5.392
r_scangle_other5.263
r_scbond_it3.761
r_scbond_other3.76
r_mcangle_it3.342
r_mcangle_other3.342
r_mcbond_it2.367
r_mcbond_other2.366
r_angle_refined_deg1.566
r_angle_other_deg1.231
r_chiral_restr0.102
r_bond_refined_d0.016
r_gen_planes_refined0.01
r_bond_other_d0.006
r_gen_planes_other0.005
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1822
Nucleic Acid Atoms
Solvent Atoms246
Heterogen Atoms56

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing