3CY6

Crystal Structure of E18Q DJ-1


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52981.5 M sodium citrate, 50 mM HEPES, 10 mM DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.957.61

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.78α = 90
b = 74.78β = 90
c = 75.443γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315BENT CONICAL Si MIRROR (Rh COATED)2006-03-11MSINGLE 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)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
11.353098.60.07325.27.15340053400
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.351.498.70.6072.34.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTpdb entry 1P5F1.35305333750614272398.540.155160.154440.16837RANDOM13.051
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]
0.190.090.19-0.28
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.031
r_dihedral_angle_4_deg21.942
r_dihedral_angle_3_deg12.596
r_dihedral_angle_1_deg6.39
r_scangle_it4.765
r_scbond_it3.679
r_mcangle_it2.647
r_mcbond_it2.387
r_angle_refined_deg1.428
r_angle_other_deg0.817
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.031
r_dihedral_angle_4_deg21.942
r_dihedral_angle_3_deg12.596
r_dihedral_angle_1_deg6.39
r_scangle_it4.765
r_scbond_it3.679
r_mcangle_it2.647
r_mcbond_it2.387
r_angle_refined_deg1.428
r_angle_other_deg0.817
r_symmetry_hbond_refined0.36
r_mcbond_other0.32
r_symmetry_vdw_other0.297
r_xyhbond_nbd_refined0.29
r_nbd_refined0.251
r_symmetry_vdw_refined0.231
r_nbd_other0.213
r_nbtor_refined0.175
r_chiral_restr0.093
r_nbtor_other0.091
r_bond_refined_d0.014
r_gen_planes_refined0.006
r_gen_planes_other0.002
r_bond_other_d
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1418
Nucleic Acid Atoms
Solvent Atoms193
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing