3DML

Crystal structure of the periplasmic thioredoxin SoxS from Paracoccus pantotrophus (reduced form)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.42910.1M citrate, 0.4M sodium phosphate, 0.4M potassium phosphate, 3% (w/v) glucose, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.3647.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.909α = 90
b = 80.909β = 90
c = 33.212γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDmirrors2006-09-22MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X120.95369, 0.97833, 0.97838, 1.0332EMBL/DESY, HamburgX12

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.920.7199.30.0830.08330.876.310064999818.37
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.91.9497.90.4470.4476.365.1662

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMADTHROUGHOUT1.920.719557953048099.720.156680.156680.15440.20124RANDOM22.168
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]
0.30.150.3-0.45
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.723
r_dihedral_angle_4_deg19.553
r_dihedral_angle_3_deg15.954
r_dihedral_angle_1_deg5.667
r_scangle_it4.157
r_scbond_it2.847
r_mcangle_it1.738
r_mcbond_it1.659
r_angle_refined_deg1.512
r_nbtor_refined0.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.723
r_dihedral_angle_4_deg19.553
r_dihedral_angle_3_deg15.954
r_dihedral_angle_1_deg5.667
r_scangle_it4.157
r_scbond_it2.847
r_mcangle_it1.738
r_mcbond_it1.659
r_angle_refined_deg1.512
r_nbtor_refined0.32
r_nbd_refined0.225
r_symmetry_vdw_refined0.216
r_symmetry_hbond_refined0.214
r_xyhbond_nbd_refined0.192
r_chiral_restr0.098
r_bond_refined_d0.012
r_gen_planes_refined0.006
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 Atoms799
Nucleic Acid Atoms
Solvent Atoms162
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
MAR345data collection
DENZOdata reduction
SCALEPACKdata scaling
Auto-Rickshawphasing