6DXN

1.95 Angstrom Resolution Crystal Structure of DsbA Disulfide Interchange Protein from Klebsiella pneumoniae.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4OCF 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.5292Protein: 9.6mg/ml, 0.01M Tris-HCl pH 8.3; Screen: PEGs II (B9), 0.1M Tris-HCl pH 8.5, 30% (v/v) PEG 400.
Crystal Properties
Matthews coefficientSolvent content
2.1542.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.401α = 90.27
b = 42.392β = 89.78
c = 103.949γ = 96
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDC(111)2018-04-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.97872APS21-ID-F

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)Rrim I (All)Rpim I (All)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
11.953097.80.1350.1350.1540.07316.84.451946-318.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.951.9896.30.7860.7860.8970.430.7262.74.3

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 REPLACEMENTTHROUGHOUT4OCF1.9527.0148932239796.410.182130.179730.22982RANDOM22.852
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]
-0.3612.880.653.66-13.9-3.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.586
r_dihedral_angle_3_deg9.702
r_dihedral_angle_4_deg8.881
r_long_range_B_refined4.329
r_long_range_B_other4.232
r_dihedral_angle_1_deg2.712
r_mcangle_it2.599
r_mcangle_other2.598
r_scangle_other2.387
r_mcbond_it1.671
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.586
r_dihedral_angle_3_deg9.702
r_dihedral_angle_4_deg8.881
r_long_range_B_refined4.329
r_long_range_B_other4.232
r_dihedral_angle_1_deg2.712
r_mcangle_it2.599
r_mcangle_other2.598
r_scangle_other2.387
r_mcbond_it1.671
r_mcbond_other1.67
r_scbond_it1.625
r_scbond_other1.624
r_angle_refined_deg1.133
r_angle_other_deg0.427
r_chiral_restr0.056
r_gen_planes_refined0.038
r_gen_planes_other0.034
r_bond_refined_d0.006
r_bond_other_d0.001
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6032
Nucleic Acid Atoms
Solvent Atoms365
Heterogen Atoms30

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
MrBUMPphasing