3QJ6

The crystal structure of PWWP domain of human Hepatoma-derived growth factor 2 in complex with H3K79me3 peptide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3EAEpdb entry 3eae

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION2932.0M ammonium sulfate, 5% isopropanol. Protein was pre-incubated with 5 equivalents of peptide ligand, VAPOR DIFFUSION, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.160

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.934α = 90
b = 74.934β = 90
c = 41.764γ = 120
Symmetry
Space GroupP 61

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152009-04-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-C0.97944APS24-ID-C

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
12.3401000.08511.610.86094
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)
12.32.341000.46610.4313

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 3eae2.337.468606328199.8020.2360.23370.276RANDOM37.022
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]
1.7070.8531.707-2.56
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.778
r_dihedral_angle_4_deg14.903
r_dihedral_angle_3_deg13.072
r_dihedral_angle_1_deg6.758
r_scangle_it1.708
r_angle_refined_deg1.173
r_scbond_it1.079
r_angle_other_deg0.792
r_mcangle_it0.783
r_mcbond_it0.419
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.778
r_dihedral_angle_4_deg14.903
r_dihedral_angle_3_deg13.072
r_dihedral_angle_1_deg6.758
r_scangle_it1.708
r_angle_refined_deg1.173
r_scbond_it1.079
r_angle_other_deg0.792
r_mcangle_it0.783
r_mcbond_it0.419
r_chiral_restr0.07
r_mcbond_other0.069
r_bond_refined_d0.011
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms764
Nucleic Acid Atoms
Solvent Atoms10
Heterogen Atoms7

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling