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Crystal structure of Amacstatin-1, a cystatin from the hard tick Amblyomma maculatum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6ZTK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 291 0.2 M ammonium phosphate, 0.1 M Tris-HCl pH 8.5, 50% (v/v) MPD
Crystal Properties Matthews coefficient Solvent content 3.28 62.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.411 α = 90 b = 98.411 β = 90 c = 27.579 γ = 120
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 2020-01-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.541870
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.807 42.61 92.1 0.068 0.998 80.7 4.5 13304
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.807 1.84 21.5 0.129 0.177 0.965 1.3
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.807 28.425 13190 686 91.737 0.163 0.161 0.1623 0.2023 0.2039 21.061
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] 0.769 0.384 0.769 -2.493
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.724 r_dihedral_angle_3_deg 14.428 r_dihedral_angle_2_deg 9.996 r_lrange_it 6.936 r_dihedral_angle_1_deg 6.826 r_lrange_other 6.718 r_scangle_it 5.18 r_scangle_other 5.092 r_scbond_it 3.469 r_scbond_other 3.404
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.724 r_dihedral_angle_3_deg 14.428 r_dihedral_angle_2_deg 9.996 r_lrange_it 6.936 r_dihedral_angle_1_deg 6.826 r_lrange_other 6.718 r_scangle_it 5.18 r_scangle_other 5.092 r_scbond_it 3.469 r_scbond_other 3.404 r_mcangle_other 3.361 r_mcangle_it 3.331 r_mcbond_it 2.314 r_mcbond_other 2.185 r_angle_refined_deg 1.51 r_angle_other_deg 0.508 r_symmetry_nbd_other 0.205 r_nbd_refined 0.194 r_nbtor_refined 0.175 r_xyhbond_nbd_refined 0.154 r_symmetry_nbd_refined 0.146 r_nbd_other 0.136 r_symmetry_xyhbond_nbd_refined 0.122 r_symmetry_nbtor_other 0.086 r_chiral_restr 0.07 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 817 Nucleic Acid Atoms Solvent Atoms 141 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing