5SY6

Atomic resolution structure of human DJ-1, DTT bound


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1P5F 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.529823-27% PEG 3000, 100 mM HEPES, 200 mM NaCl, 10 mM dithiothreitol (DTT)
Crystal Properties
Matthews coefficientSolvent content
3.0659.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.227α = 90
b = 75.227β = 90
c = 75.227γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315bent conical Si, Rh coated2006-06-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 14-BM-C0.9APS14-BM-C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)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
11.15491000.088116.311.187636
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.151.1799.71.6670.6141.78.4

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 REPLACEMENTTHROUGHOUT1P5F1.154983306429699.990.110670.109710.12948RANDOM18.749
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]
-0.04-0.02-0.040.14
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free51.923
r_dihedral_angle_2_deg34.166
r_dihedral_angle_4_deg20.794
r_sphericity_bonded15.704
r_dihedral_angle_3_deg11.062
r_long_range_B_refined7.322
r_long_range_B_other7.32
r_dihedral_angle_1_deg5.929
r_scangle_other3.549
r_scbond_it3.113
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free51.923
r_dihedral_angle_2_deg34.166
r_dihedral_angle_4_deg20.794
r_sphericity_bonded15.704
r_dihedral_angle_3_deg11.062
r_long_range_B_refined7.322
r_long_range_B_other7.32
r_dihedral_angle_1_deg5.929
r_scangle_other3.549
r_scbond_it3.113
r_scbond_other3.112
r_rigid_bond_restr2.746
r_mcangle_other2.589
r_mcangle_it2.588
r_mcbond_other1.913
r_mcbond_it1.905
r_angle_refined_deg1.675
r_angle_other_deg1.041
r_chiral_restr0.117
r_bond_refined_d0.013
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1374
Nucleic Acid Atoms
Solvent Atoms256
Heterogen Atoms8

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
Aimlessdata scaling
PHASERphasing