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Crystal structure of thioredoxin reductase from Cryptosporidium parvum in the "activated in" conformation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9G92
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 294.15 0.1 M Tris/HCl, 0.1 M KSCN, PEG 2000 MME, 5 mM DTT
Crystal Properties Matthews coefficient Solvent content 2.34 47.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.872 α = 90 b = 72.543 β = 90.613 c = 188.458 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 2024-09-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 1.0 ELETTRA 11.2C
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 2.4 39.91 99.53 0.12 0.996 12.72 6.5 78143
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.486 0.78 0.79
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.4 39.91 78128 3930 99.681 0.225 0.2232 0.2568 0.2487 40.311
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] 0.36 -0.404 -1.098 0.747
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.701 r_dihedral_angle_4_deg 18.173 r_dihedral_angle_3_deg 15.034 r_dihedral_angle_1_deg 7.47 r_dihedral_angle_other_3_deg 6.872 r_lrange_it 5.265 r_lrange_other 5.264 r_scangle_it 3.369 r_scangle_other 3.369 r_mcangle_it 3.229
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.701 r_dihedral_angle_4_deg 18.173 r_dihedral_angle_3_deg 15.034 r_dihedral_angle_1_deg 7.47 r_dihedral_angle_other_3_deg 6.872 r_lrange_it 5.265 r_lrange_other 5.264 r_scangle_it 3.369 r_scangle_other 3.369 r_mcangle_it 3.229 r_mcangle_other 3.229 r_scbond_other 2.079 r_scbond_it 2.078 r_mcbond_it 2.007 r_mcbond_other 2.006 r_angle_refined_deg 1.533 r_angle_other_deg 1.274 r_nbd_other 0.331 r_symmetry_nbd_refined 0.282 r_symmetry_xyhbond_nbd_refined 0.217 r_nbd_refined 0.199 r_symmetry_nbd_other 0.187 r_nbtor_refined 0.162 r_xyhbond_nbd_refined 0.151 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.073 r_symmetry_xyhbond_nbd_other 0.061 r_ncsr_local_group_1 0.051 r_ncsr_local_group_4 0.05 r_ncsr_local_group_3 0.048 r_ncsr_local_group_6 0.048 r_ncsr_local_group_2 0.043 r_ncsr_local_group_5 0.041 r_bond_refined_d 0.01 r_bond_other_d 0.006 r_gen_planes_refined 0.006 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15073 Nucleic Acid Atoms Solvent Atoms 284 Heterogen Atoms 247
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing