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Crystal structure of Iristatin, a secreted salivary cystatin from the hard tick Ixodes ricinus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3L0R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 288.15 0.1 M Bis-Tris buffer, pH 5.5
1 M ammonium sulphate
1% (w/v) PEG 3350
mother liquor: protein ratio 1.5:1
Crystal Properties Matthews coefficient Solvent content 2.5 50.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.033 α = 90 b = 76.929 β = 90 c = 92.122 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 PIXEL DECTRIS PILATUS 6M 2016-04-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.9184 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.76 59.05 97.84 0.038 0.044 1 19.32 3.73 27677 36.75
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.76 1.87 96.8 0.71 0.83 0.76 1.56 3.69
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 3L0R 1.76 59.05 26286 1384 97.84 0.1941 0.19089 0.1972 0.25572 0.2557 RANDOM 41.036
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 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.489 r_dihedral_angle_4_deg 14.676 r_dihedral_angle_3_deg 13.639 r_dihedral_angle_1_deg 7.71 r_long_range_B_refined 7.486 r_long_range_B_other 7.485 r_mcangle_other 1.761 r_mcangle_it 1.757 r_angle_refined_deg 1.722 r_scangle_other 1.282
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.489 r_dihedral_angle_4_deg 14.676 r_dihedral_angle_3_deg 13.639 r_dihedral_angle_1_deg 7.71 r_long_range_B_refined 7.486 r_long_range_B_other 7.485 r_mcangle_other 1.761 r_mcangle_it 1.757 r_angle_refined_deg 1.722 r_scangle_other 1.282 r_mcbond_it 0.997 r_mcbond_other 0.972 r_angle_other_deg 0.947 r_scbond_it 0.79 r_scbond_other 0.788 r_chiral_restr 0.096 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1858 Nucleic Acid Atoms Solvent Atoms 241 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement XDS data reduction PHASER phasing