2IN3

Crystal structure of a putative protein disulfide isomerase from Nitrosomonas europaea


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP729325mM Potassium phosphate, 20% PEG 8000, 2% Tacsimate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.5151.09

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.844α = 90
b = 59.642β = 90
c = 84.45γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152005-10-16MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.97930, 0.97946APS19-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.8531.9940.05711.58.22039120391-347.8
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.851.9267.70.334.4

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 DIFFRACTIONMADTHROUGHOUT1.8531.91934019340105093.970.190530.190530.18860.22731RANDOM48
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]
-2.772.20.57
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.409
r_dihedral_angle_4_deg17.644
r_dihedral_angle_3_deg12.797
r_dihedral_angle_1_deg5.175
r_scangle_it3.261
r_scbond_it2.117
r_angle_refined_deg1.358
r_mcangle_it1.276
r_mcbond_it0.957
r_nbtor_refined0.312
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.409
r_dihedral_angle_4_deg17.644
r_dihedral_angle_3_deg12.797
r_dihedral_angle_1_deg5.175
r_scangle_it3.261
r_scbond_it2.117
r_angle_refined_deg1.358
r_mcangle_it1.276
r_mcbond_it0.957
r_nbtor_refined0.312
r_symmetry_vdw_refined0.209
r_nbd_refined0.208
r_xyhbond_nbd_refined0.154
r_symmetry_hbond_refined0.145
r_chiral_restr0.093
r_bond_refined_d0.014
r_gen_planes_refined0.007
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 Atoms1631
Nucleic Acid Atoms
Solvent Atoms180
Heterogen Atoms27

Software

Software
Software NamePurpose
REFMACrefinement
SBC-Collectdata collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
autoSHARPphasing
ARP/wARPmodel building
Cootmodel building