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Crystal structure of Iripin-5 serpin from Ixodes ricinus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NDA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 277 Magnesium Chloride hexahydrate, Tris, PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.05 39.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.239 α = 90 b = 63.778 β = 116.78 c = 81.994 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 PILATUS3 6M 2020-07-15 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) 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 1.495 48.09 98.7 0.998 11.17 11 112133
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 1.5 1.59 0.613
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 3NDA 1.5 48.09 110024 2101 98.85 0.1533 0.1528 0.1526 0.1836 0.1829 RANDOM 17.71
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 -0.44 -0.25 0.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.46 r_dihedral_angle_4_deg 19.879 r_dihedral_angle_3_deg 12.648 r_dihedral_angle_1_deg 7.001 r_angle_refined_deg 1.65 r_angle_other_deg 1.537 r_chiral_restr 0.084 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.46 r_dihedral_angle_4_deg 19.879 r_dihedral_angle_3_deg 12.648 r_dihedral_angle_1_deg 7.001 r_angle_refined_deg 1.65 r_angle_other_deg 1.537 r_chiral_restr 0.084 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5848 Nucleic Acid Atoms Solvent Atoms 1089 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XDS data scaling MOLREP phasing