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Crystal Structure of Cyclophilin TgCyp23 from Toxoplasma gondii in complex with dihydro Cyclosporin A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8B58
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 0.1M citric acid pH 3.5, and 25% polyethylene glycol 3350
Crystal Properties Matthews coefficient Solvent content 2.18 43.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.346 α = 90 b = 118.109 β = 103.67 c = 47.46 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 PILATUS 6M 2023-09-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.979260 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.2 42.96 98.67 0.046 0.019 0.999 16.8 6.8 125896 15.96
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.2 1.243 97.04 1.028 0.418 0.752 1.45 6.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.2 42.96 1.34 125841 6379 98.67 0.1723 0.1716 0.1809 0.1866 0.1917 22.07
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 22.5863 f_angle_d 1.5224 f_chiral_restr 0.0886 f_bond_d 0.0113 f_plane_restr 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3080 Nucleic Acid Atoms Solvent Atoms 448 Heterogen Atoms 170
Software Software Software Name Purpose REFMAC refinement PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing