3BHN

Crystal structure of a dj-1/pfpi-like protein (shew_2856) from shewanella loihica pv-4 at 1.76 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.2277NANODROP, 0.2M Na Tartrate, 20.0% PEG 3350, No Buffer pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.5151.05

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.32α = 90
b = 71.32β = 90
c = 180.63γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152007-10-04MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.20.9537, 0.9798, 0.9796ALS8.2.2

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
11.7629.22399.40.08313.1410.3527863-322.32
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)
11.761.8295.40.8062

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONMADTHROUGHOUT1.7629.22327782139899.880.1630.1620.19RANDOM18.478
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]
0.590.30.59-0.89
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.769
r_dihedral_angle_4_deg20.813
r_dihedral_angle_3_deg12.681
r_scangle_it6.046
r_dihedral_angle_1_deg4.968
r_scbond_it4.785
r_mcangle_it2.502
r_mcbond_it1.862
r_angle_refined_deg1.397
r_angle_other_deg0.984
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.769
r_dihedral_angle_4_deg20.813
r_dihedral_angle_3_deg12.681
r_scangle_it6.046
r_dihedral_angle_1_deg4.968
r_scbond_it4.785
r_mcangle_it2.502
r_mcbond_it1.862
r_angle_refined_deg1.397
r_angle_other_deg0.984
r_mcbond_other0.461
r_symmetry_hbond_refined0.219
r_nbd_refined0.213
r_nbd_other0.192
r_xyhbond_nbd_refined0.177
r_nbtor_refined0.174
r_symmetry_vdw_refined0.169
r_symmetry_vdw_other0.158
r_chiral_restr0.092
r_nbtor_other0.089
r_bond_refined_d0.015
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1604
Nucleic Acid Atoms
Solvent Atoms204
Heterogen Atoms12

Software

Software
Software NamePurpose
REFMACrefinement
PHENIXrefinement
SOLVEphasing
MolProbitymodel building
XSCALEdata scaling
PDB_EXTRACTdata extraction
ADSCdata collection
XDSdata reduction