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Unreduced cathepsin V in complex with stefin A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3H6S 3h6s, 1nb3 experimental model PDB 1NB3 3h6s, 1nb3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 0.1M Tris-HCl, 12% PEG3000, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.63 53.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.313 α = 90 b = 107.29 β = 90 c = 115.98 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 MAR CCD 165 mm Collimating and focusing, Pt-coated mirrors 2008-05-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 5.2R 1.00 ELETTRA 5.2R
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 1.99 22 99.5 0.079 8 8.2 51300 51049 1 1
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) 2 2.03 91.5 0.43 6.8 2302
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 3h6s, 1nb3 1.99 19.49 51180 50986 2586 99.62 0.182 0.178 0.176 0.1745 0.219 0.2145 RANDOM 32.922
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] 0.49 -1.21 0.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.793 r_dihedral_angle_3_deg 14.578 r_dihedral_angle_4_deg 14.293 r_dihedral_angle_1_deg 5.555 r_scangle_it 4.123 r_scbond_it 2.615 r_mcangle_it 1.607 r_angle_refined_deg 1.578 r_mcbond_it 0.916 r_chiral_restr 0.128
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.793 r_dihedral_angle_3_deg 14.578 r_dihedral_angle_4_deg 14.293 r_dihedral_angle_1_deg 5.555 r_scangle_it 4.123 r_scbond_it 2.615 r_mcangle_it 1.607 r_angle_refined_deg 1.578 r_mcbond_it 0.916 r_chiral_restr 0.128 r_bond_refined_d 0.018 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4932 Nucleic Acid Atoms Solvent Atoms 722 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection AMoRE phasing