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Monoclinic form of papain/ZLFG-DAM covalent complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PPN PDB ENTRY 1PPN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9.2 292 68% methanol/ethanol (2:1), 34 mM NaCl, 50 mM 2-aminoethanol/HCl, pH 9.2, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.12 42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.44 α = 90 b = 48.93 β = 112.42 c = 52.69 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 293 IMAGE PLATE MARRESEARCH 1998-03-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE MACSCIENCE 1.5418
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 2 20 88.9 0.123 6.6 4.8 12041 12041 -3 -3 26.2
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 2 2.07 75.1 0.328 2 1.74
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 (All) 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 1PPN 2 10 10783 10783 1165 88.8 0.185 0.185 0.18 0.212 0.229 0.25 RANDOM 22.1
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] -1.22 0.12 0.57 0.74
RMS Deviations Key Refinement Restraint Deviation p_scangle_it 3.784 p_scbond_it 2.451 p_angle_deg 1.663 p_mcangle_it 1.3 p_mcbond_it 0.793 p_chiral_restr 0.108 p_angle_d 0.025 p_bond_d 0.016 p_plane_restr 0.007 p_planar_d
RMS Deviations Key Refinement Restraint Deviation p_scangle_it 3.784 p_scbond_it 2.451 p_angle_deg 1.663 p_mcangle_it 1.3 p_mcbond_it 0.793 p_chiral_restr 0.108 p_angle_d 0.025 p_bond_d 0.016 p_plane_restr 0.007 p_planar_d p_hb_or_metal_coord p_singtor_nbd p_multtor_nbd p_xhyhbond_nbd p_xyhbond_nbd p_planar_tor p_staggered_tor p_orthonormal_tor p_transverse_tor p_special_tor
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1679 Nucleic Acid Atoms Solvent Atoms 53 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling AMoRE phasing REFMAC refinement