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Crystal Structure of Lactococcus lactis Thioredoxin Reductase (FO conformation)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4GCM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 292 20% PEG4000, 400 mM Li2SO4.
DTT added (20 mM DTT final in drop)
Crystal Properties Matthews coefficient Solvent content 2.48 50.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.61 α = 90 b = 132.26 β = 112.62 c = 73.5 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 CCD MARMOSAIC 225 mm CCD 2014-11-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I911-3 1.0 MAX II I911-3
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 47.36 99 0.088 0.997 12.18 3.9 86685
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 2.05 98.4 0.826 0.633 1.82 3.9
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 4GCM 2 47.36 82350 4335 99.14 0.2322 0.2299 0.2344 0.276 0.2791 RANDOM 34.646
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] -1.04 -1.05 2.38 -0.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.882 r_dihedral_angle_4_deg 22.524 r_dihedral_angle_3_deg 14.293 r_dihedral_angle_1_deg 6.44 r_angle_refined_deg 1.699 r_angle_other_deg 1.069 r_chiral_restr 0.092 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_gen_planes_other 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.882 r_dihedral_angle_4_deg 22.524 r_dihedral_angle_3_deg 14.293 r_dihedral_angle_1_deg 6.44 r_angle_refined_deg 1.699 r_angle_other_deg 1.069 r_chiral_restr 0.092 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_gen_planes_other 0.004 r_bond_other_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9356 Nucleic Acid Atoms Solvent Atoms 409 Heterogen Atoms 232
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling MOLREP phasing