6AFD

DJ-1 with compound 6


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
3.160.34

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.39α = 90
b = 75.39β = 90
c = 75.29γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2702013-10-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NE3A1.000Photon FactoryAR-NE3A

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
11.4832.61000.0960.99712.17.241594
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)
11.481.561000.6870.7662.56.7

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 REPLACEMENTTHROUGHOUT1SOA1.4832.640258130099.980.119670.118920.14344RANDOM17.981
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]
0.050.030.05-0.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.943
r_sphericity_free32.298
r_dihedral_angle_4_deg18.776
r_dihedral_angle_3_deg13.059
r_sphericity_bonded10.323
r_dihedral_angle_1_deg6.383
r_long_range_B_refined4.315
r_rigid_bond_restr3.966
r_scangle_other3.542
r_long_range_B_other3.487
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.943
r_sphericity_free32.298
r_dihedral_angle_4_deg18.776
r_dihedral_angle_3_deg13.059
r_sphericity_bonded10.323
r_dihedral_angle_1_deg6.383
r_long_range_B_refined4.315
r_rigid_bond_restr3.966
r_scangle_other3.542
r_long_range_B_other3.487
r_scbond_it3.167
r_scbond_other3.165
r_mcangle_other2.08
r_mcangle_it2.035
r_angle_refined_deg1.662
r_mcbond_it1.655
r_mcbond_other1.551
r_angle_other_deg0.879
r_chiral_restr0.109
r_bond_refined_d0.016
r_gen_planes_refined0.009
r_bond_other_d0.001
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 Atoms245
Heterogen Atoms24

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing