☰ Navigation Tabs
Re-determination of the native structure of human dipeptidyl peptidase I (cathepsin C)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1K3B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.4 298 1.8M ammonium sulfate, 0.1M Na citrate, 0.2M Na/K tartrate, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.8 56.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.479 α = 90 b = 88.68 β = 90 c = 114.35 γ = 90
Symmetry Space Group I 2 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 120 IMAGE PLATE MAR scanner 345 mm plate 2004-08-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.05 30 120690 120690
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.05 2.12 96.1
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 1k3b 2.05 24.04 25787 25787 1376 96.11 0.17612 0.17612 0.17375 0.1815 0.22076 0.2343 RANDOM 23.055
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] 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 8.872 r_scangle_it 4.066 r_scbond_it 2.66 r_mcangle_it 1.993 r_angle_refined_deg 1.849 r_mcbond_it 1.115 r_angle_other_deg 0.978 r_symmetry_vdw_other 0.264 r_nbd_other 0.256 r_nbd_refined 0.239
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 8.872 r_scangle_it 4.066 r_scbond_it 2.66 r_mcangle_it 1.993 r_angle_refined_deg 1.849 r_mcbond_it 1.115 r_angle_other_deg 0.978 r_symmetry_vdw_other 0.264 r_nbd_other 0.256 r_nbd_refined 0.239 r_xyhbond_nbd_refined 0.185 r_symmetry_hbond_refined 0.15 r_chiral_restr 0.137 r_symmetry_vdw_refined 0.131 r_nbtor_other 0.09 r_bond_refined_d 0.02 r_gen_planes_refined 0.01 r_gen_planes_other 0.007 r_bond_other_d 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other 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 2720 Nucleic Acid Atoms Solvent Atoms 211 Heterogen Atoms 100
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling