2OQ7

The crystal structure of JMJD2A complexed with Ni and N-oxalylglycine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2GP3PDB entry 2gp3

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.527720% PEG 3350, 0.1M citrate, 2 mM NiCl2, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.4349.32

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 101.12α = 90
b = 148.531β = 90
c = 57.333γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2006-09-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA0.99900SLSX10SA

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
12.1559.8794.50.07810.43.2450234502336
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)
12.152.2796.50.4852.13.26601

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB entry 2gp32.15504307243072191294.060.178760.178760.176540.228RANDOM29.938
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]
-0.35-0.81.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.465
r_dihedral_angle_4_deg17.523
r_dihedral_angle_3_deg15.496
r_scangle_it7.292
r_dihedral_angle_1_deg6.832
r_scbond_it6.068
r_mcangle_it3.972
r_mcbond_it2.9
r_angle_refined_deg1.583
r_angle_other_deg0.981
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.465
r_dihedral_angle_4_deg17.523
r_dihedral_angle_3_deg15.496
r_scangle_it7.292
r_dihedral_angle_1_deg6.832
r_scbond_it6.068
r_mcangle_it3.972
r_mcbond_it2.9
r_angle_refined_deg1.583
r_angle_other_deg0.981
r_mcbond_other0.841
r_symmetry_hbond_refined0.231
r_symmetry_vdw_other0.209
r_nbd_refined0.199
r_nbd_other0.191
r_nbtor_refined0.186
r_symmetry_vdw_refined0.147
r_xyhbond_nbd_refined0.146
r_chiral_restr0.095
r_nbtor_other0.091
r_metal_ion_refined0.064
r_bond_refined_d0.017
r_xyhbond_nbd_other0.008
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5536
Nucleic Acid Atoms
Solvent Atoms204
Heterogen Atoms24

Software

Software
Software NamePurpose
REFMACrefinement
MAR345data collection
MOSFLMdata reduction
CCP4data scaling