6AFJ

DJ-1 with compound 13


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.5293.15100mM TRIS-HCl, 200mM sodium citrate, 30% PEG 400, 5mM DTT
Crystal Properties
Matthews coefficientSolvent content
3.1160.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.14α = 90
b = 75.14β = 90
c = 75.91γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152014-11-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-5A1.000Photon FactoryBL-5A

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
11.4833.799.90.0790.99813.5741703
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)
11.481.5699.70.7970.7492.26.6

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 REPLACEMENTTHROUGHOUT1SOA1.4833.739996168299.910.140730.139480.17168RANDOM22.364
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]
0.180.090.18-0.58
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.108
r_sphericity_free27.604
r_dihedral_angle_4_deg17.246
r_sphericity_bonded14.138
r_dihedral_angle_3_deg12.309
r_dihedral_angle_1_deg6.173
r_long_range_B_refined4.483
r_long_range_B_other4.332
r_scangle_other3.967
r_rigid_bond_restr3.712
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.108
r_sphericity_free27.604
r_dihedral_angle_4_deg17.246
r_sphericity_bonded14.138
r_dihedral_angle_3_deg12.309
r_dihedral_angle_1_deg6.173
r_long_range_B_refined4.483
r_long_range_B_other4.332
r_scangle_other3.967
r_rigid_bond_restr3.712
r_scbond_it3.486
r_scbond_other3.483
r_mcangle_it3.094
r_mcangle_other3.083
r_mcbond_it2.663
r_mcbond_other2.632
r_angle_refined_deg1.664
r_angle_other_deg0.98
r_chiral_restr0.096
r_bond_refined_d0.013
r_gen_planes_refined0.008
r_bond_other_d0.004
r_gen_planes_other0.001
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 Atoms1376
Nucleic Acid Atoms
Solvent Atoms172
Heterogen Atoms20

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing