5FE1

Crystal structure of human PCAF bromodomain in complex with fragment BR004 (fragment 1)


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
3.5265.09

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 99.67α = 90
b = 99.67β = 90
c = 100.4γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2011-09-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E SUPERBRIGHT1.54178

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
12.2233.471000.09211.24.41835243.5
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)
12.222.341000.72824.3

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 3GG32.2233.471740094099.910.209910.208310.24083RANDOM44.942
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]
-0.1-0.05-0.10.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.941
r_dihedral_angle_4_deg19.2
r_dihedral_angle_3_deg13.899
r_dihedral_angle_1_deg5.89
r_long_range_B_refined5.387
r_long_range_B_other5.387
r_scangle_other2.774
r_mcangle_it2.14
r_mcangle_other2.139
r_scbond_it1.647
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.941
r_dihedral_angle_4_deg19.2
r_dihedral_angle_3_deg13.899
r_dihedral_angle_1_deg5.89
r_long_range_B_refined5.387
r_long_range_B_other5.387
r_scangle_other2.774
r_mcangle_it2.14
r_mcangle_other2.139
r_scbond_it1.647
r_scbond_other1.645
r_angle_refined_deg1.496
r_angle_other_deg1.385
r_mcbond_other1.281
r_mcbond_it1.28
r_chiral_restr0.097
r_bond_refined_d0.014
r_gen_planes_refined0.008
r_bond_other_d0.007
r_gen_planes_other0.007
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 Atoms1780
Nucleic Acid Atoms
Solvent Atoms153
Heterogen Atoms28

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing