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The crystal structure of rhodesain, the major cysteine protease of T. brucei rhodesiense, bound to inhibitor K777
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1F2A 1F2A WITHOUT INHIBITOR OR WATERS, WITH SIDE CHAINS THAT DIFFER CUT BACK TO ALANINE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 291 1.0 M Sodium citrate; imidazole pH 8.00, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 1.96 37.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.377 α = 120.38 b = 39.716 β = 93.89 c = 39.566 γ = 101.18
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 298 IMAGE PLATE RIGAKU RAXIS IV MIRRORS 2000-05-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200
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 1.65 30 89.7 0.047 1.8 18751
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) 1.65 1.7 83.7 0.147
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 1F2A WITHOUT INHIBITOR OR WATERS, WITH SIDE CHAINS THAT DIFFER CUT BACK TO ALANINE 1.65 19.46 51956 17747 950 89.47 0.137 0.135 0.1448 0.175 0.1822 RANDOM 13.33
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] 0.26 0.17 0.51 -0.41 0.28 0.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.843 r_dihedral_angle_4_deg 20.611 r_dihedral_angle_3_deg 12.812 r_dihedral_angle_1_deg 5.671 r_scangle_it 4.593 r_scbond_it 3.17 r_mcangle_it 1.904 r_angle_refined_deg 1.673 r_angle_other_deg 1.665 r_mcbond_it 1.543
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.843 r_dihedral_angle_4_deg 20.611 r_dihedral_angle_3_deg 12.812 r_dihedral_angle_1_deg 5.671 r_scangle_it 4.593 r_scbond_it 3.17 r_mcangle_it 1.904 r_angle_refined_deg 1.673 r_angle_other_deg 1.665 r_mcbond_it 1.543 r_mcbond_other 0.344 r_symmetry_vdw_other 0.277 r_symmetry_hbond_refined 0.248 r_symmetry_vdw_refined 0.244 r_nbd_refined 0.209 r_nbd_other 0.193 r_nbtor_refined 0.182 r_xyhbond_nbd_refined 0.177 r_chiral_restr 0.11 r_nbtor_other 0.094 r_bond_refined_d 0.02 r_gen_planes_refined 0.008 r_bond_other_d 0.003 r_gen_planes_other 0.001 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 Atoms Number Protein Atoms 1626 Nucleic Acid Atoms Solvent Atoms 169 Heterogen Atoms 41
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing