2OS2

Crystal structure of JMJD2A complexed with histone H3 peptide trimethylated at Lys36


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2OQ7PDB entry 2oq7

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.527720% PEG 3350, 0.1 M Citrate, 2 mM NiCl2, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.3547.57

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.943α = 90
b = 148.886β = 90
c = 56.975γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS HTC2007-01-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.54180

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
12.33098.40.059203.8383243832447
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.4293.31.93.65187

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB entry 2oq72.3303666536665160898.170.178630.178630.176490.22552RANDOM29.484
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]
-1.170.071.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.405
r_dihedral_angle_4_deg16.941
r_dihedral_angle_3_deg14.552
r_scangle_it7.436
r_scbond_it6.388
r_dihedral_angle_1_deg6.314
r_mcangle_it4.117
r_mcbond_it3.068
r_angle_refined_deg1.4
r_angle_other_deg0.93
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.405
r_dihedral_angle_4_deg16.941
r_dihedral_angle_3_deg14.552
r_scangle_it7.436
r_scbond_it6.388
r_dihedral_angle_1_deg6.314
r_mcangle_it4.117
r_mcbond_it3.068
r_angle_refined_deg1.4
r_angle_other_deg0.93
r_mcbond_other0.45
r_symmetry_hbond_refined0.211
r_symmetry_vdw_other0.187
r_nbd_other0.186
r_nbd_refined0.185
r_nbtor_refined0.181
r_xyhbond_nbd_refined0.149
r_symmetry_vdw_refined0.126
r_nbtor_other0.087
r_chiral_restr0.082
r_bond_refined_d0.013
r_gen_planes_refined0.005
r_bond_other_d0.002
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 Atoms5740
Nucleic Acid Atoms
Solvent Atoms210
Heterogen Atoms24

Software

Software
Software NamePurpose
REFMACrefinement
CrystalCleardata collection
MOSFLMdata reduction
CCP4data scaling