3ZLI

Crystal structure of JmjC domain of human histone demethylase UTY


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3AVSPDB ENTRY 3AVS

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2770.2M TRIMETHYLAMINE N-OXIDE; 0.1M HEPES PH 7.5; 10%(W/V) PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.6954.31

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.585α = 90
b = 110.249β = 90
c = 118.242γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2012-12-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I03DiamondI03

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
11.849.961000.07213.46.71101472
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)
11.81.831000.926.9

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 3AVS1.850.01104567549499.970.177410.175990.20435RANDOM32.803
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]
-1.69-0.051.74
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.318
r_dihedral_angle_4_deg18.821
r_dihedral_angle_3_deg11.83
r_dihedral_angle_1_deg5.889
r_mcangle_it2.632
r_scbond_it2.559
r_mcbond_it1.845
r_mcbond_other1.843
r_angle_refined_deg1.533
r_angle_other_deg1.081
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.318
r_dihedral_angle_4_deg18.821
r_dihedral_angle_3_deg11.83
r_dihedral_angle_1_deg5.889
r_mcangle_it2.632
r_scbond_it2.559
r_mcbond_it1.845
r_mcbond_other1.843
r_angle_refined_deg1.533
r_angle_other_deg1.081
r_chiral_restr0.097
r_bond_refined_d0.014
r_gen_planes_refined0.009
r_bond_other_d0.005
r_gen_planes_other0.005
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7027
Nucleic Acid Atoms
Solvent Atoms549
Heterogen Atoms80

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing