3B36

Structure of M26L DJ-1


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.529830% PEG 3000, 100 mM HEPES, 200 mM NaCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 7.50
Crystal Properties
Matthews coefficientSolvent content
3.0159.18

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.818α = 90
b = 74.818β = 90
c = 75.264γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110IMAGE PLATERIGAKU RAXIS IV++2007-09-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007

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
11.564.8299.90.06936.89.839440
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)
1.51.5599.90.16138.9

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 REPLACEMENTTHROUGHOUT1P5F1.564.823743337433197699.910.166330.165880.17486RANDOM13.105
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]
0.140.070.14-0.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.425
r_dihedral_angle_4_deg16.895
r_dihedral_angle_3_deg10.745
r_dihedral_angle_1_deg5.63
r_scangle_it2.613
r_scbond_it1.609
r_angle_refined_deg1.165
r_mcangle_it0.904
r_mcbond_it0.631
r_nbtor_refined0.303
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.425
r_dihedral_angle_4_deg16.895
r_dihedral_angle_3_deg10.745
r_dihedral_angle_1_deg5.63
r_scangle_it2.613
r_scbond_it1.609
r_angle_refined_deg1.165
r_mcangle_it0.904
r_mcbond_it0.631
r_nbtor_refined0.303
r_nbd_refined0.208
r_symmetry_vdw_refined0.208
r_xyhbond_nbd_refined0.126
r_symmetry_hbond_refined0.102
r_chiral_restr0.072
r_bond_refined_d0.007
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1468
Nucleic Acid Atoms
Solvent Atoms211
Heterogen Atoms33

Software

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