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Papain bound to a natural cysteine protease inhibitor from Streptomyces mobaraensis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9PAP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 100 mM HEPES pH 7.5 and 80% 2-Methyl-2,4-pentanediol (MPD)
Crystal Properties Matthews coefficient Solvent content 2.18 43.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.644 α = 90 b = 48.921 β = 90 c = 101.547 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 PIXEL DECTRIS PILATUS 6M 2018-02-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.97242 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) CC (Half) 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 50.65 99.8 0.026 0.999 15.1 13.1 26295
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.65 1.68 0.252 0.876
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 9PAP 1.65 44.112 26239 1325 99.749 0.198 0.1964 0.2069 0.2214 0.2251 24.649
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] -0.312 1.251 -0.939
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.326 r_dihedral_angle_4_deg 15.895 r_dihedral_angle_other_3_deg 12.97 r_dihedral_angle_3_deg 10.435 r_dihedral_angle_1_deg 6.009 r_lrange_other 3.28 r_lrange_it 3.277 r_scangle_it 2.028 r_scangle_other 2.027 r_mcangle_other 1.503
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.326 r_dihedral_angle_4_deg 15.895 r_dihedral_angle_other_3_deg 12.97 r_dihedral_angle_3_deg 10.435 r_dihedral_angle_1_deg 6.009 r_lrange_other 3.28 r_lrange_it 3.277 r_scangle_it 2.028 r_scangle_other 2.027 r_mcangle_other 1.503 r_mcangle_it 1.501 r_scbond_it 1.258 r_scbond_other 1.258 r_angle_other_deg 1.207 r_angle_refined_deg 1.175 r_mcbond_it 0.912 r_mcbond_other 0.907 r_nbd_other 0.188 r_nbd_refined 0.173 r_nbtor_refined 0.166 r_symmetry_nbd_other 0.165 r_symmetry_xyhbond_nbd_refined 0.135 r_xyhbond_nbd_refined 0.103 r_symmetry_nbtor_other 0.073 r_symmetry_nbd_refined 0.067 r_chiral_restr 0.05 r_gen_planes_refined 0.004 r_bond_refined_d 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1636 Nucleic Acid Atoms Solvent Atoms 107 Heterogen Atoms 59
Software Software Software Name Purpose REFMAC refinement autoXDS data reduction Aimless data scaling MOLREP phasing