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Crystal structure of domain swapped dimer of Amacstatin-2, a cystatin from the hard tick Amblyomma maculatum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold G3MQC0 N-terminus truncated to Gly29
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 291 0.1 M bicine-Tris-HCl pH 8.5, 12.5% w/v PEG 1000, 12.5% (w/v) PEG 3350, 12.5% (v/v) MPD, 0.3 M diethyleneglycol, 0.3 M triethyleneglycol, 0.3 M tetraethyleneglycol, and 0.3 M pentaethyleneglycol
Crystal Properties Matthews coefficient Solvent content 2.05 40.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.172 α = 90 b = 49.172 β = 90 c = 86.458 γ = 90
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 2019-10-04 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) 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 2.146 49.172 92.28 0.116 0.1256 0.04719 0.997 10.34 6.8 10697 44.96
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 2.146 2.227 61.42 5.08 5.828 2.766 0.396 4.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.146 49.172 10385 520 92.155 0.228 0.2257 0.2175 0.2746 0.266 Random selection 49.134
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] 0.617 0.617 -1.235
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.874 r_dihedral_angle_6_deg 14.978 r_dihedral_angle_2_deg 12.698 r_lrange_it 10.269 r_lrange_other 10.266 r_scangle_it 8.3 r_scangle_other 8.296 r_dihedral_angle_1_deg 7.781 r_mcangle_it 7.429 r_mcangle_other 7.426
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.874 r_dihedral_angle_6_deg 14.978 r_dihedral_angle_2_deg 12.698 r_lrange_it 10.269 r_lrange_other 10.266 r_scangle_it 8.3 r_scangle_other 8.296 r_dihedral_angle_1_deg 7.781 r_mcangle_it 7.429 r_mcangle_other 7.426 r_scbond_it 5.687 r_scbond_other 5.683 r_mcbond_it 5.205 r_mcbond_other 5.202 r_angle_refined_deg 1.62 r_angle_other_deg 0.535 r_xyhbond_nbd_refined 0.321 r_nbd_refined 0.223 r_symmetry_nbd_other 0.218 r_nbd_other 0.197 r_nbtor_refined 0.183 r_ncsr_local_group_1 0.147 r_symmetry_nbtor_other 0.091 r_chiral_restr 0.07 r_symmetry_nbd_refined 0.048 r_symmetry_xyhbond_nbd_refined 0.031 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1613 Nucleic Acid Atoms Solvent Atoms 3 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing