5SYA

Atomic resolution structure of D24N mutant human DJ-1


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.529823-27% polyethylene glycol (PEG) 4000, 0.2 M Sodium Citrate, and 0.1 M Tris HCl
Crystal Properties
Matthews coefficientSolvent content
3.0259.28

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.969α = 90
b = 74.969β = 90
c = 75.336γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MRh coated collimating mirror, K-B focusing mirrors2016-02-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-20.88SSRLBL9-2

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
11.13899.80.042120.45.598874
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)
11.11.1297.10.9190.7381.85.4

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 REPLACEMENTTHROUGHOUT1p5f1.13893885494099.730.113870.113170.12765RANDOM16.762
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]
0.130.070.13-0.43
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free44.178
r_dihedral_angle_2_deg35.087
r_dihedral_angle_4_deg19.112
r_sphericity_bonded12.384
r_dihedral_angle_3_deg11.372
r_dihedral_angle_1_deg5.992
r_long_range_B_refined4.344
r_rigid_bond_restr3.942
r_long_range_B_other3.565
r_scangle_other3.127
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free44.178
r_dihedral_angle_2_deg35.087
r_dihedral_angle_4_deg19.112
r_sphericity_bonded12.384
r_dihedral_angle_3_deg11.372
r_dihedral_angle_1_deg5.992
r_long_range_B_refined4.344
r_rigid_bond_restr3.942
r_long_range_B_other3.565
r_scangle_other3.127
r_scbond_it2.584
r_scbond_other2.576
r_mcangle_other2.083
r_mcangle_it2.075
r_mcbond_it1.725
r_angle_refined_deg1.699
r_mcbond_other1.68
r_angle_other_deg1.029
r_chiral_restr0.138
r_bond_refined_d0.015
r_gen_planes_refined0.009
r_bond_other_d0.003
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 Atoms1372
Nucleic Acid Atoms
Solvent Atoms230
Heterogen Atoms8

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing