3GN3

Crystal structure of a putative protein-disulfide isomerase from Pseudomonas syringae to 2.5A resolution.


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52890.1M Hepes pH 7.5, 2M Ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
4.8474.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 151.968α = 90
b = 151.968β = 90
c = 115.894γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM Q215rmirrors2009-03-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-BM0.97974APS19-BM

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
12.5501000.14296277392772122
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)
12.52.591000.7466

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Cut-off Sigma (I)Cut-off Sigma (F)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 DIFFRACTIONSADTHROUGHOUT2.549.752226297139399.870.20780.207280.205680.23692RANDOM40.831
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_deg37.289
r_dihedral_angle_4_deg19.194
r_dihedral_angle_3_deg17.312
r_dihedral_angle_1_deg5.956
r_scangle_it3.096
r_scbond_it1.853
r_angle_refined_deg1.352
r_mcangle_it1.063
r_mcbond_it0.533
r_chiral_restr0.094
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.289
r_dihedral_angle_4_deg19.194
r_dihedral_angle_3_deg17.312
r_dihedral_angle_1_deg5.956
r_scangle_it3.096
r_scbond_it1.853
r_angle_refined_deg1.352
r_mcangle_it1.063
r_mcbond_it0.533
r_chiral_restr0.094
r_bond_refined_d0.012
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2762
Nucleic Acid Atoms
Solvent Atoms93
Heterogen Atoms17

Software

Software
Software NamePurpose
SBC-Collectdata collection
HKL-3000phasing
SHELXmodel building
MLPHAREphasing
DMmodel building
ARP/wARPmodel building
Cootmodel building
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
SHELXphasing
DMphasing