2OX0

Crystal structure of JMJD2A complexed with histone H3 peptide dimethylated at Lys9


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.52770.1M Citrate, 4mM NiCl2, 20% PEG 3350, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.448.78

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 101.21α = 90
b = 150.004β = 90
c = 57.228γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2007-02-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA0.91820SLSX10SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.9541.4999.60.0720.084123.664355640972
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.952.0698.40.5890.69923.39121

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.9541.496137061370267999.490.170470.170470.168710.20999RANDOM29.491
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]
-0.8-0.120.93
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.61
r_dihedral_angle_4_deg13.077
r_dihedral_angle_3_deg12.843
r_dihedral_angle_1_deg5.924
r_scangle_it5.276
r_scbond_it3.801
r_mcangle_it2.584
r_mcbond_it1.802
r_angle_refined_deg1.139
r_angle_other_deg0.857
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.61
r_dihedral_angle_4_deg13.077
r_dihedral_angle_3_deg12.843
r_dihedral_angle_1_deg5.924
r_scangle_it5.276
r_scbond_it3.801
r_mcangle_it2.584
r_mcbond_it1.802
r_angle_refined_deg1.139
r_angle_other_deg0.857
r_mcbond_other0.481
r_nbd_refined0.199
r_symmetry_hbond_refined0.191
r_nbtor_refined0.181
r_nbd_other0.178
r_symmetry_vdw_other0.165
r_xyhbond_nbd_refined0.127
r_symmetry_vdw_refined0.103
r_nbtor_other0.087
r_chiral_restr0.07
r_bond_refined_d0.009
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5737
Nucleic Acid Atoms
Solvent Atoms483
Heterogen Atoms25

Software

Software
Software NamePurpose
REFMACrefinement
CrystalCleardata collection
MOSFLMdata reduction
CCP4data scaling
PHASERphasing