5SY9

Atomic resolution structure of E15Q 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 DROP8.529825-28% PEG 4000, 0.1 M Tris HCl, 0.1 M sodium citrate
Crystal Properties
Matthews coefficientSolvent content
2.8356.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 86.276α = 90
b = 121.963β = 90
c = 43.512γ = 90
Symmetry
Space GroupC 2 2 21

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
11.13798.10.070.99914.95.191327
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)
11.11.1285.41.0660.5691.43.8

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 REPLACEMENTTHROUGHOUT1p5f1.13788556275197.910.118370.117770.13735RANDOM13.225
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]
0.35-0.440.1
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free49.608
r_dihedral_angle_2_deg42.483
r_dihedral_angle_4_deg17.445
r_sphericity_bonded13.182
r_dihedral_angle_3_deg11.549
r_long_range_B_refined8.63
r_dihedral_angle_1_deg6.327
r_long_range_B_other5.384
r_rigid_bond_restr2.126
r_angle_refined_deg1.821
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free49.608
r_dihedral_angle_2_deg42.483
r_dihedral_angle_4_deg17.445
r_sphericity_bonded13.182
r_dihedral_angle_3_deg11.549
r_long_range_B_refined8.63
r_dihedral_angle_1_deg6.327
r_long_range_B_other5.384
r_rigid_bond_restr2.126
r_angle_refined_deg1.821
r_scangle_other1.572
r_scbond_other1.393
r_scbond_it1.392
r_mcangle_other1.229
r_mcangle_it1.214
r_angle_other_deg1.046
r_mcbond_it0.852
r_mcbond_other0.809
r_chiral_restr0.117
r_bond_refined_d0.014
r_gen_planes_refined0.01
r_gen_planes_other0.003
r_bond_other_d0.002
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 Atoms1385
Nucleic Acid Atoms
Solvent Atoms308
Heterogen Atoms20

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing