2QSA

Crystal structure of J-domain of DnaJ homolog dnj-2 precursor from C.elegans.


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72872.5 M NaCl, 0.1 M Tris buffer pH 7.0, 0.2 M MgCl2, VAPOR DIFFUSION, SITTING DROP, temperature 287K
Crystal Properties
Matthews coefficientSolvent content
2.957.58

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.148α = 90
b = 81.148β = 90
c = 60.016γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152007-02-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.97920APS19-ID

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
11.6827.797.50.04533.75.3163891638932.9
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)
11.681.7274.80.4791.942.9848

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 2O371.6827.7155581555882997.550.16390.16390.16310.1803RANDOM23.524
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]
0.380.190.38-0.57
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.92
r_dihedral_angle_4_deg17.767
r_dihedral_angle_3_deg14.01
r_dihedral_angle_1_deg5.043
r_scangle_it3.521
r_scbond_it2.451
r_mcangle_it1.496
r_angle_refined_deg1.462
r_mcbond_it1.067
r_nbtor_refined0.311
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.92
r_dihedral_angle_4_deg17.767
r_dihedral_angle_3_deg14.01
r_dihedral_angle_1_deg5.043
r_scangle_it3.521
r_scbond_it2.451
r_mcangle_it1.496
r_angle_refined_deg1.462
r_mcbond_it1.067
r_nbtor_refined0.311
r_symmetry_hbond_refined0.266
r_nbd_refined0.247
r_xyhbond_nbd_refined0.166
r_symmetry_vdw_refined0.147
r_chiral_restr0.122
r_bond_refined_d0.017
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 Atoms871
Nucleic Acid Atoms
Solvent Atoms109
Heterogen Atoms1

Software

Software
Software NamePurpose
REFMACrefinement
SBC-Collectdata collection
HKL-2000data reduction
HKL-3000data scaling
PHASERphasing