2OT7

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


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, 100 mM Citrate, 2 mM NiCl, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.4148.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 101.209α = 90
b = 149.842β = 90
c = 57.47γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152007-02-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-11.0723ESRFID23-1

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
12.13583.9299.10.07211.92.9487844878438
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)
12.1352.251000.541237095

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 2OQ72.135204591445914203197.20.189090.189090.186760.24072RANDOM32.416
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]
-0.970.040.93
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.971
r_dihedral_angle_3_deg14.422
r_dihedral_angle_4_deg14.22
r_dihedral_angle_1_deg6.566
r_scangle_it6.362
r_scbond_it5.165
r_mcangle_it3.331
r_mcbond_it2.384
r_angle_refined_deg1.33
r_angle_other_deg0.897
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.971
r_dihedral_angle_3_deg14.422
r_dihedral_angle_4_deg14.22
r_dihedral_angle_1_deg6.566
r_scangle_it6.362
r_scbond_it5.165
r_mcangle_it3.331
r_mcbond_it2.384
r_angle_refined_deg1.33
r_angle_other_deg0.897
r_mcbond_other0.632
r_symmetry_vdw_other0.252
r_symmetry_hbond_refined0.232
r_symmetry_vdw_refined0.198
r_nbd_refined0.196
r_nbd_other0.183
r_nbtor_refined0.183
r_xyhbond_nbd_refined0.157
r_nbtor_other0.085
r_chiral_restr0.077
r_metal_ion_refined0.039
r_bond_refined_d0.012
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
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 Atoms5730
Nucleic Acid Atoms
Solvent Atoms263
Heterogen Atoms24

Software

Software
Software NamePurpose
REFMACrefinement
DNAdata collection
MOSFLMdata reduction
CCP4data scaling