3DXU

The crystal structure of core JMJD2D complexed with FE and N-oxalylglycine


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5278Ammonium sulfate, pH6.50, VAPOR DIFFUSION, HANGING DROP, temperature 278K
Crystal Properties
Matthews coefficientSolvent content
2.4850.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.543α = 90
b = 71.543β = 90
c = 150.194γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray130CCD2007-02-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.11.00ALS8.2.1

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
12.2502234420644

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT2.247.9519398104599.380.170.1680.221RANDOM15.142
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]
0.790.79-1.57
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.175
r_dihedral_angle_4_deg25.059
r_dihedral_angle_3_deg17.858
r_dihedral_angle_1_deg6.763
r_scangle_it4.061
r_scbond_it2.789
r_angle_refined_deg1.936
r_mcangle_it1.607
r_mcbond_it1.072
r_symmetry_hbond_refined0.504
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.175
r_dihedral_angle_4_deg25.059
r_dihedral_angle_3_deg17.858
r_dihedral_angle_1_deg6.763
r_scangle_it4.061
r_scbond_it2.789
r_angle_refined_deg1.936
r_mcangle_it1.607
r_mcbond_it1.072
r_symmetry_hbond_refined0.504
r_nbtor_refined0.313
r_nbd_refined0.226
r_xyhbond_nbd_refined0.222
r_symmetry_vdw_refined0.215
r_chiral_restr0.128
r_bond_refined_d0.022
r_gen_planes_refined0.008
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2692
Nucleic Acid Atoms
Solvent Atoms365
Heterogen Atoms45

Software

Software
Software NamePurpose
MOLREPphasing
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling