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Cathepsin B in complex with stefin A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NB3 PDB ENTRY 1NB3 and 1SP4 experimental model PDB 1SP4 PDB ENTRY 1NB3 and 1SP4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.2M ammonium suphate, 24% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.71 27.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.122 α = 89.95 b = 31.078 β = 104.45 c = 70.937 γ = 89.9
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 Double Crystal Si111 2009-03-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 5.2R 0.99988 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 2.6 50 92.6 0.084 6 2.6 15513 14361 2 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 2.6 2.64 71.2 0.206 2.2 564
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 PDB ENTRY 1NB3 and 1SP4 2.61 40.52 15513 14360 713 92.1 0.201 0.198 0.1967 0.25 0.2422 RANDOM 42.42
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] -3.46 -1.31 -4.29 4.54 -1.65 -3.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.572 r_dihedral_angle_4_deg 24.331 r_dihedral_angle_3_deg 22.513 r_dihedral_angle_1_deg 7.197 r_scangle_it 2.723 r_angle_refined_deg 1.709 r_scbond_it 1.586 r_mcangle_it 1.478 r_mcbond_it 0.79 r_chiral_restr 0.119
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.572 r_dihedral_angle_4_deg 24.331 r_dihedral_angle_3_deg 22.513 r_dihedral_angle_1_deg 7.197 r_scangle_it 2.723 r_angle_refined_deg 1.709 r_scbond_it 1.586 r_mcangle_it 1.478 r_mcbond_it 0.79 r_chiral_restr 0.119 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5454 Nucleic Acid Atoms Solvent Atoms 127 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