3EEB

Structure of the V. cholerae RTX cysteine protease domain


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.529530% PEG3350, 15% MPD, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.244.15

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.491α = 90
b = 66.099β = 90
c = 136.051γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray140CCDMARMOSAIC 325 mm CCD2008-01-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL11-11.000SSRLBL11-1

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
12.13096.30.1176.32371325.7
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)
2.12.1897.40.533.25.52347

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 DIFFRACTIONSADTHROUGHOUT2.13022101117896.310.20150.199320.24279RANDOM28.879
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]
1-2.721.71
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.113
r_dihedral_angle_4_deg14.975
r_dihedral_angle_3_deg13.257
r_dihedral_angle_1_deg5.757
r_scangle_it2.78
r_scbond_it1.756
r_angle_refined_deg1.333
r_mcangle_it1.266
r_mcbond_it0.676
r_symmetry_hbond_refined0.341
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.113
r_dihedral_angle_4_deg14.975
r_dihedral_angle_3_deg13.257
r_dihedral_angle_1_deg5.757
r_scangle_it2.78
r_scbond_it1.756
r_angle_refined_deg1.333
r_mcangle_it1.266
r_mcbond_it0.676
r_symmetry_hbond_refined0.341
r_nbtor_refined0.297
r_metal_ion_refined0.277
r_symmetry_vdw_refined0.235
r_nbd_refined0.198
r_xyhbond_nbd_refined0.153
r_chiral_restr0.076
r_bond_refined_d0.01
r_gen_planes_refined0.004
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_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 Atoms3116
Nucleic Acid Atoms
Solvent Atoms224
Heterogen Atoms74

Software

Software
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling