2P7U

The crystal structure of rhodesain, the major cysteine protease of T. brucei rhodesiense, bound to inhibitor K777


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP82911.0 M Sodium citrate; imidazole pH 8.00, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
1.9637.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 34.377α = 120.38
b = 39.716β = 93.89
c = 39.566γ = 101.18
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298IMAGE PLATERIGAKU RAXIS IVMIRRORS2000-05-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU200

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
11.653089.70.0471.818751
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)
1.651.783.70.147

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1F2A WITHOUT INHIBITOR OR WATERS, WITH SIDE CHAINS THAT DIFFER CUT BACK TO ALANINE1.6519.46519561774795089.470.1370.1350.175RANDOM13.33
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]
0.260.170.51-0.410.280.57
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.843
r_dihedral_angle_4_deg20.611
r_dihedral_angle_3_deg12.812
r_dihedral_angle_1_deg5.671
r_scangle_it4.593
r_scbond_it3.17
r_mcangle_it1.904
r_angle_refined_deg1.673
r_angle_other_deg1.665
r_mcbond_it1.543
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.843
r_dihedral_angle_4_deg20.611
r_dihedral_angle_3_deg12.812
r_dihedral_angle_1_deg5.671
r_scangle_it4.593
r_scbond_it3.17
r_mcangle_it1.904
r_angle_refined_deg1.673
r_angle_other_deg1.665
r_mcbond_it1.543
r_mcbond_other0.344
r_symmetry_vdw_other0.277
r_symmetry_hbond_refined0.248
r_symmetry_vdw_refined0.244
r_nbd_refined0.209
r_nbd_other0.193
r_nbtor_refined0.182
r_xyhbond_nbd_refined0.177
r_chiral_restr0.11
r_nbtor_other0.094
r_bond_refined_d0.02
r_gen_planes_refined0.008
r_bond_other_d0.003
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 Atoms1626
Nucleic Acid Atoms
Solvent Atoms169
Heterogen Atoms41

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing