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Structure of Echinococcus multilocularis Cystatin B
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5ZC1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 289.15 30% PEG400
100 mM Tris base/ Hydrochloric acid pH 8.5
200 mM Magnesium chloride
Crystal Properties Matthews coefficient Solvent content 2.26 45.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.773 α = 90 b = 66.112 β = 103.432 c = 92.6 γ = 90
Symmetry Space Group P 1 21 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 EIGER2 X 9M 2022-09-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL02U1 0.979 SSRF BL02U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.999 50 98.9 0.104 29.371 5.9 57418
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.999 2.03 0.822
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 THROUGHOUT 1.999 37.247 57401 2798 98.812 0.212 0.2107 0.2165 0.2405 0.2426 42.232
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] -2.656 0.3 4.918 -2.158
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.462 r_dihedral_angle_6_deg 15.689 r_dihedral_angle_2_deg 14.083 r_lrange_other 10.976 r_lrange_it 10.971 r_scangle_it 8.226 r_scangle_other 8.225 r_dihedral_angle_1_deg 7.37 r_mcangle_it 5.547 r_mcangle_other 5.546
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.462 r_dihedral_angle_6_deg 15.689 r_dihedral_angle_2_deg 14.083 r_lrange_other 10.976 r_lrange_it 10.971 r_scangle_it 8.226 r_scangle_other 8.225 r_dihedral_angle_1_deg 7.37 r_mcangle_it 5.547 r_mcangle_other 5.546 r_scbond_it 5.29 r_scbond_other 5.289 r_mcbond_it 3.744 r_mcbond_other 3.744 r_angle_refined_deg 1.751 r_angle_other_deg 0.631 r_nbd_other 0.228 r_nbd_refined 0.225 r_symmetry_nbd_other 0.211 r_ncsr_local_group_6 0.193 r_symmetry_xyhbond_nbd_refined 0.188 r_ncsr_local_group_24 0.186 r_ncsr_local_group_26 0.183 r_xyhbond_nbd_refined 0.181 r_ncsr_local_group_21 0.18 r_symmetry_nbd_refined 0.178 r_ncsr_local_group_12 0.177 r_ncsr_local_group_28 0.171 r_nbtor_refined 0.168 r_ncsr_local_group_17 0.168 r_ncsr_local_group_2 0.14 r_ncsr_local_group_5 0.135 r_ncsr_local_group_20 0.131 r_ncsr_local_group_3 0.129 r_ncsr_local_group_16 0.129 r_ncsr_local_group_14 0.127 r_ncsr_local_group_19 0.126 r_ncsr_local_group_1 0.125 r_ncsr_local_group_15 0.125 r_ncsr_local_group_4 0.124 r_ncsr_local_group_7 0.124 r_ncsr_local_group_9 0.123 r_ncsr_local_group_8 0.122 r_ncsr_local_group_23 0.121 r_ncsr_local_group_27 0.12 r_ncsr_local_group_10 0.116 r_ncsr_local_group_18 0.109 r_ncsr_local_group_25 0.108 r_ncsr_local_group_13 0.106 r_symmetry_xyhbond_nbd_other 0.104 r_chiral_restr 0.1 r_ncsr_local_group_22 0.091 r_symmetry_nbtor_other 0.087 r_ncsr_local_group_11 0.067 r_bond_refined_d 0.007 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 6276 Nucleic Acid Atoms Solvent Atoms 361 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing