2QW4

Human NR4A1 ligand-binding domain


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.830015 % PEG 6000, 0.1 M BISTRIS PH 6.4, 0.4 M SODIUM THIOCYANATE, AND 5 % ETHYLENGLYCOL, pH 6.80, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Crystal Properties
Matthews coefficientSolvent content
2.6353.15

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.53α = 90
b = 96.364β = 90
c = 144.849γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42006-02-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 17-ID1.0APS17-ID

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
12.810098.931070
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.82.9100

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 REPLACEMENTTHROUGHOUT1yje2.848.1729394156698.50.2330.230.292RANDOM55.78
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]
-0.150.61-0.47
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.58
r_dihedral_angle_3_deg21.785
r_dihedral_angle_4_deg21.171
r_dihedral_angle_1_deg6.837
r_scangle_it2.795
r_scbond_it1.695
r_angle_refined_deg1.635
r_mcangle_it1.148
r_mcbond_it0.63
r_nbtor_refined0.317
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.58
r_dihedral_angle_3_deg21.785
r_dihedral_angle_4_deg21.171
r_dihedral_angle_1_deg6.837
r_scangle_it2.795
r_scbond_it1.695
r_angle_refined_deg1.635
r_mcangle_it1.148
r_mcbond_it0.63
r_nbtor_refined0.317
r_symmetry_vdw_refined0.313
r_symmetry_hbond_refined0.253
r_nbd_refined0.245
r_xyhbond_nbd_refined0.138
r_chiral_restr0.104
r_bond_refined_d0.015
r_gen_planes_refined0.005
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 Atoms7137
Nucleic Acid Atoms
Solvent Atoms10
Heterogen Atoms

Software

Software
Software NamePurpose
PHASERphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling