4IGO

Histone H3 Lysine 4 Demethylating rice Rice JMJ703 in complex with alpha-KG


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5291potassium phosphate monobasic, 25% (w/v) polyethylene glycol 8000 , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.244.03

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.518α = 90
b = 90.518β = 90
c = 76.048γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayCCDMAR CCD 165 mm2012-01-03MSINGLE WAVELENGTH
21CCDADSC QUANTUM 3152012-01-11
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBSRF BEAMLINE 1W2B1.0000BSRF1W2B
2SYNCHROTRONSSRF BEAMLINE BL17U1.0000SSRFBL17U

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.45099.51624915149

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)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 DIFFRACTIONMOLECULAR REPLACEMENT2OQ62.438.8921.35151491393868499.920.19660.19520.19340.2299random
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]
5.47055.4705-10.9409
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d16.843
f_angle_d1.268
f_chiral_restr0.092
f_bond_d0.009
f_plane_restr0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2208
Nucleic Acid Atoms
Solvent Atoms89
Heterogen Atoms11

Software

Software
Software NamePurpose
HKL-2000data collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling