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Tick salivary cystatin Ricistatin in complex with cathepsin V
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3KFQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 291.15 0.07 M Ammonium acetate 4.5 18.9% w/v PEG 10,000
Crystal Properties Matthews coefficient Solvent content 2.01 38.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.488 α = 90 b = 45.322 β = 96.89 c = 58.52 γ = 90
Symmetry Space Group C 1 2 1
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 300K 2021-02-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.541870
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.92 43.91 99.2 0.132 0.16 0.09 0.991 6.5 3.1 23406
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.92 1.97 94 1.07 1.362 0.828 0.32 2.2
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 (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 3kfq 1.92 43.87 22253 1153 99.07 0.1878 0.1859 0.1953 0.2261 0.2273 RANDOM 27.591
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] -0.57 -0.92 1.57 -0.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.636 r_dihedral_angle_4_deg 19.779 r_dihedral_angle_3_deg 14.362 r_dihedral_angle_1_deg 7.037 r_angle_refined_deg 1.462 r_angle_other_deg 1.317 r_chiral_restr 0.065 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.636 r_dihedral_angle_4_deg 19.779 r_dihedral_angle_3_deg 14.362 r_dihedral_angle_1_deg 7.037 r_angle_refined_deg 1.462 r_angle_other_deg 1.317 r_chiral_restr 0.065 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2277 Nucleic Acid Atoms Solvent Atoms 188 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement XDS data reduction PDB_EXTRACT data extraction Aimless data scaling MOLREP phasing