3UYJ

Crystal structure of JMJD5 catalytic core domain in complex with nickle and alpha-KG


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1EVAPORATION7.52918% PEG3350, 0.1M HepesNa pH 7.5, EVAPORATION, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
3.1460.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.393α = 90
b = 68.393β = 90
c = 266.686γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDADSC QUANTUM 315mirrors2011-11-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U0.97922SSRFBL17U

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
12.352098.830.06722.64.73117430809-342.86
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)
12.352.39990.3354.8

Refinement

Statistics
Diffraction IDStructure Solution MethodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONSAD2.35119.9943117430809156498.830.20540.20290.2531
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]
6.42716.4271-12.8543
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d16.611
f_angle_d1.058
f_chiral_restr0.078
f_bond_d0.013
f_plane_restr0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3837
Nucleic Acid Atoms
Solvent Atoms209
Heterogen Atoms22

Software

Software
Software NamePurpose
CBASSdata collection
SOLVEphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling