4UF0

Crystal structure of JmjC domain of human histone demethylase UTY in complex with epitherapuetic compound 2-(((2-((2-(dimethylamino)ethyl) (ethyl)amino)-2-oxoethyl)amino)methyl)isonicotinic acid.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3ZLIPDB ENTRY 3ZLI

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.525% PEG3350, 0.1M BIS-TRIS PH 6.5
Crystal Properties
Matthews coefficientSolvent content
2.8356.56

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.494α = 90
b = 110.458β = 90
c = 119.23γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray287CCDADSC CCDADSC QUANTUM 3152014-11-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I02DiamondI02

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
11.7881.0399.90.0619.516.71147712
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)
11.781.8499.90.062.866.8

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 3ZLI1.7881.03109117565099.970.151840.148570.21517RANDOM36.64
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]
-1.630.491.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.489
r_sphericity_free28.313
r_sphericity_bonded18.008
r_dihedral_angle_4_deg15.561
r_dihedral_angle_3_deg13.89
r_scbond_it7.072
r_dihedral_angle_1_deg6.389
r_mcangle_it6.02
r_rigid_bond_restr5.478
r_mcbond_it5.359
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.489
r_sphericity_free28.313
r_sphericity_bonded18.008
r_dihedral_angle_4_deg15.561
r_dihedral_angle_3_deg13.89
r_scbond_it7.072
r_dihedral_angle_1_deg6.389
r_mcangle_it6.02
r_rigid_bond_restr5.478
r_mcbond_it5.359
r_mcbond_other5.358
r_angle_refined_deg1.714
r_angle_other_deg0.909
r_chiral_restr0.101
r_bond_refined_d0.017
r_gen_planes_refined0.007
r_bond_other_d0.003
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7058
Nucleic Acid Atoms
Solvent Atoms488
Heterogen Atoms128

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
CCP4Iphasing