3QZV

Crystal Structure of BPTF PHD-linker-bromo in complex with histone H4K12ac peptide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2F6JPDB ENTRY 2F6J

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.529320% (W/V) PEG3000, 0.3 M NaAcetate, 0.1 M Na-Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.4249.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.525α = 90
b = 38.513β = 111.2
c = 87.752γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDADSC QUANTUM 3152009-10-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29A1.0809NSLSX29A

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
11.9992098.20.06110.87.313759
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)
11.9992.0596.20.5067.1878

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 ENTRY 2F6J1.9992013758104498.080.18630.18230.2342RANDOM42.786
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]
-0.750.591.95-0.78
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.028
r_dihedral_angle_3_deg15.731
r_dihedral_angle_4_deg11.741
r_dihedral_angle_1_deg4.805
r_scangle_it2.78
r_scbond_it1.664
r_angle_refined_deg1.159
r_mcangle_it0.984
r_mcbond_it0.511
r_chiral_restr0.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.028
r_dihedral_angle_3_deg15.731
r_dihedral_angle_4_deg11.741
r_dihedral_angle_1_deg4.805
r_scangle_it2.78
r_scbond_it1.664
r_angle_refined_deg1.159
r_mcangle_it0.984
r_mcbond_it0.511
r_chiral_restr0.08
r_bond_refined_d0.011
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1418
Nucleic Acid Atoms
Solvent Atoms142
Heterogen Atoms2

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction