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The high resolution x-ray structure of papain complexed with fragments of the Trypanosoma brucei cysteine protease inhibitor ICP.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9PAP PDB ENTRY 9PAP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 50% ETHANOL, 0.01M NA ACETATE, pH 7.50
Crystal Properties Matthews coefficient Solvent content 2.2 44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.323 α = 90 b = 46.118 β = 90 c = 95.697 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 CCD TOROIDAL MIRRORS 2005-12-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 ESRF ID29
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 1.5 95.7 100 0.1 21.4 13.6 60928 2 16.24
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 1.5 1.58 100 0.63 3.7 13.8
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 PDB ENTRY 9PAP 1.5 95.7 30823 1551 100 0.179 0.177 0.1749 0.225 0.223 RANDOM 19.83
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] -0.739 0.764 -0.025
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.339 r_dihedral_angle_4_deg 17.949 r_dihedral_angle_3_deg 13.97 r_dihedral_angle_1_deg 5.617 r_scangle_it 3.424 r_scbond_it 2.911 r_mcangle_it 2.065 r_angle_refined_deg 1.416 r_mcbond_it 1.366 r_nbtor_refined 0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.339 r_dihedral_angle_4_deg 17.949 r_dihedral_angle_3_deg 13.97 r_dihedral_angle_1_deg 5.617 r_scangle_it 3.424 r_scbond_it 2.911 r_mcangle_it 2.065 r_angle_refined_deg 1.416 r_mcbond_it 1.366 r_nbtor_refined 0.32 r_nbd_refined 0.234 r_symmetry_vdw_refined 0.23 r_symmetry_hbond_refined 0.221 r_xyhbond_nbd_refined 0.205 r_chiral_restr 0.098 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1690 Nucleic Acid Atoms Solvent Atoms 161 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing