2P86

The high resolution crystal structure of rhodesain, the major cathepsin L protease from T. brucei rhodesiense, bound to inhibitor K11002


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
192981.6M Ammonium Sulfate, 0.1 M Bicine pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.3447.34

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 33.659α = 90
b = 78.628β = 90
c = 80.725γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315FLAT MIRROR, RH COATED2005-07-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-1SSRLBL9-1

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
11.1640.3691.90.04327.27.168633
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)
1.161.22800.1214.96.9

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 REPLACEMENTTHROUGHOUT2P7U, WITHOUT WATERS OR SMALL MOLECULE INHIBITOR1.1640.3665123346391.40.1110.110.13RANDOM7.799
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]
-0.020.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.123
r_dihedral_angle_4_deg14.184
r_dihedral_angle_3_deg11.375
r_sphericity_free9.972
r_dihedral_angle_1_deg6.686
r_scangle_it4.353
r_sphericity_bonded4.308
r_scbond_it3.412
r_mcangle_it2.393
r_angle_refined_deg1.876
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.123
r_dihedral_angle_4_deg14.184
r_dihedral_angle_3_deg11.375
r_sphericity_free9.972
r_dihedral_angle_1_deg6.686
r_scangle_it4.353
r_sphericity_bonded4.308
r_scbond_it3.412
r_mcangle_it2.393
r_angle_refined_deg1.876
r_mcbond_it1.654
r_rigid_bond_restr1.654
r_angle_other_deg1.568
r_mcbond_other0.844
r_symmetry_vdw_other0.339
r_metal_ion_refined0.318
r_symmetry_vdw_refined0.294
r_xyhbond_nbd_other0.254
r_symmetry_hbond_refined0.244
r_metal_ion_other0.226
r_nbd_refined0.223
r_nbd_other0.201
r_nbtor_refined0.185
r_xyhbond_nbd_refined0.182
r_chiral_restr0.12
r_nbtor_other0.102
r_bond_refined_d0.017
r_gen_planes_refined0.013
r_bond_other_d0.002
r_gen_planes_other0.001
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1640
Nucleic Acid Atoms
Solvent Atoms402
Heterogen Atoms93

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing