6BXG

1.45 Angstrom Resolution Crystal Structure of PDZ domain of Carboxy-Terminal Protease from Vibrio cholerae in Complex with Peptide.


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.3292Protein: 9.7 mg/ml, 0.5M Sodium chloride, 0.01M Tris pH 8.3; Screen: PACT (E3) 0.2M Sodium iodide, 20% (w/v) PEG 3350..
Crystal Properties
Matthews coefficientSolvent content
1.8533.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 35.579α = 90
b = 35.579β = 90
c = 118.394γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDC(111)2017-08-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.97856APS21-ID-G

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
11.453099.90.0540.0540.0580.02151.27.415127-319.6
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)
11.451.481000.7590.7590.8170.30.8932.97.3

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 DIFFRACTIONSADTHROUGHOUT1.4529.821428870899.940.13460.13240.17758RANDOM25.91
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]
-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free28.8
r_dihedral_angle_2_deg28.59
r_dihedral_angle_4_deg19.569
r_sphericity_bonded16.515
r_rigid_bond_restr11.997
r_dihedral_angle_3_deg9.647
r_long_range_B_refined3.902
r_long_range_B_other3.779
r_dihedral_angle_1_deg3.325
r_scangle_other2.595
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free28.8
r_dihedral_angle_2_deg28.59
r_dihedral_angle_4_deg19.569
r_sphericity_bonded16.515
r_rigid_bond_restr11.997
r_dihedral_angle_3_deg9.647
r_long_range_B_refined3.902
r_long_range_B_other3.779
r_dihedral_angle_1_deg3.325
r_scangle_other2.595
r_scbond_other2.071
r_scbond_it2.07
r_mcangle_it2.05
r_mcangle_other2.049
r_mcbond_it1.612
r_mcbond_other1.612
r_angle_refined_deg1.414
r_angle_other_deg0.806
r_chiral_restr0.08
r_gen_planes_refined0.019
r_gen_planes_other0.018
r_bond_refined_d0.008
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms754
Nucleic Acid Atoms
Solvent Atoms84
Heterogen Atoms12

Software

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