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The high resolution crystal structure of rhodesain, the major cathepsin L protease from T. brucei rhodesiense, bound to inhibitor K11002
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2P7U 2P7U, WITHOUT WATERS OR SMALL MOLECULE INHIBITOR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 9 298 1.6M Ammonium Sulfate, 0.1 M Bicine pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.34 47.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.659 α = 90 b = 78.628 β = 90 c = 80.725 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315 FLAT MIRROR, RH COATED 2005-07-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-1 SSRL BL9-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.16 40.36 91.9 0.043 27.2 7.1 68633
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.16 1.22 80 0.12 14.9 6.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2P7U, WITHOUT WATERS OR SMALL MOLECULE INHIBITOR 1.16 40.36 65123 3463 91.4 0.111 0.11 0.1236 0.13 0.1412 RANDOM 7.799
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] -0.02 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.123 r_dihedral_angle_4_deg 14.184 r_dihedral_angle_3_deg 11.375 r_sphericity_free 9.972 r_dihedral_angle_1_deg 6.686 r_scangle_it 4.353 r_sphericity_bonded 4.308 r_scbond_it 3.412 r_mcangle_it 2.393 r_angle_refined_deg 1.876
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.123 r_dihedral_angle_4_deg 14.184 r_dihedral_angle_3_deg 11.375 r_sphericity_free 9.972 r_dihedral_angle_1_deg 6.686 r_scangle_it 4.353 r_sphericity_bonded 4.308 r_scbond_it 3.412 r_mcangle_it 2.393 r_angle_refined_deg 1.876 r_mcbond_it 1.654 r_rigid_bond_restr 1.654 r_angle_other_deg 1.568 r_mcbond_other 0.844 r_symmetry_vdw_other 0.339 r_metal_ion_refined 0.318 r_symmetry_vdw_refined 0.294 r_xyhbond_nbd_other 0.254 r_symmetry_hbond_refined 0.244 r_metal_ion_other 0.226 r_nbd_refined 0.223 r_nbd_other 0.201 r_nbtor_refined 0.185 r_xyhbond_nbd_refined 0.182 r_chiral_restr 0.12 r_nbtor_other 0.102 r_bond_refined_d 0.017 r_gen_planes_refined 0.013 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1640 Nucleic Acid Atoms Solvent Atoms 402 Heterogen Atoms 93
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing