2OUL

The Structure of Chagasin in Complex with a Cysteine Protease Clarifies the Binding Mode and Evolution of a New Inhibitor Family


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1727720% (v/v) PEG-300, 0.1 M Tris pH 8.5, 5% (w/v) PEG8000, and 10-15% (v/v) glycerol, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K, pH 7.00
Crystal Properties
Matthews coefficientSolvent content
3.3963.71

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 94.236α = 90
b = 94.236β = 90
c = 119.764γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray77CCDADSC QUANTUM 4MIRRORS2003-12-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.3.1ALS8.3.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.247.1296.70.0940.0912.66.3271272
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.34840.3360.3512.54.3

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 REPLACEMENTTHROUGHOUT1YVB.PDB2.247.1225763136196.750.188690.186430.23153RANDOM18.485
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]
0.230.23-0.47
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.161
r_dihedral_angle_3_deg18.119
r_dihedral_angle_4_deg15.995
r_dihedral_angle_1_deg6.58
r_scangle_it3.15
r_scbond_it2.174
r_angle_refined_deg1.519
r_mcangle_it1.27
r_mcbond_it1.013
r_angle_other_deg0.977
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.161
r_dihedral_angle_3_deg18.119
r_dihedral_angle_4_deg15.995
r_dihedral_angle_1_deg6.58
r_scangle_it3.15
r_scbond_it2.174
r_angle_refined_deg1.519
r_mcangle_it1.27
r_mcbond_it1.013
r_angle_other_deg0.977
r_symmetry_hbond_refined0.317
r_symmetry_vdw_other0.201
r_nbd_other0.194
r_nbd_refined0.192
r_nbtor_refined0.178
r_mcbond_other0.166
r_xyhbond_nbd_refined0.165
r_chiral_restr0.093
r_nbtor_other0.089
r_symmetry_vdw_refined0.03
r_bond_refined_d0.016
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2735
Nucleic Acid Atoms
Solvent Atoms171
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
ADSCdata collection