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Crystal structure of Ixodes ricinus serpin - Iripin-3
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 6.5 293.15 potassium thiocyanate, sodium cacodylate, PGA
Crystal Properties Matthews coefficient Solvent content 2.6 52.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 132.94 α = 90 b = 132.94 β = 90 c = 88.89 γ = 120
Symmetry Space Group P 62 2 2
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 2019-06-17 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 1.95 48.32 99.9 0.998 0.1345 1.573 34278
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 1.95 2.07 0.826
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 1.95 48.32 32559 1714 99.86 0.1931 0.1916 0.2001 0.2228 0.2269 RANDOM 24.264
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] 0.31 0.16 0.31 -1.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.443 r_dihedral_angle_4_deg 14.407 r_dihedral_angle_3_deg 11.268 r_dihedral_angle_1_deg 6.102 r_angle_other_deg 2.307 r_angle_refined_deg 1.709 r_chiral_restr 0.122 r_bond_other_d 0.035 r_bond_refined_d 0.015 r_gen_planes_other 0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.443 r_dihedral_angle_4_deg 14.407 r_dihedral_angle_3_deg 11.268 r_dihedral_angle_1_deg 6.102 r_angle_other_deg 2.307 r_angle_refined_deg 1.709 r_chiral_restr 0.122 r_bond_other_d 0.035 r_bond_refined_d 0.015 r_gen_planes_other 0.006 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2874 Nucleic Acid Atoms Solvent Atoms 251 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction MOLREP phasing XDS data scaling XDS data reduction