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Crystal Structure of Saccharomyces cerevisiae NDPPH Dependent Thioredoxin Reductase 1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VDC PDB ENTRY 1VDC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 6.5 291 pH 6.5, EVAPORATION, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.68 54.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.229 α = 90 b = 125.004 β = 114.16 c = 60.967 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 IMAGE PLATE MAR scanner 345 mm plate 2008-01-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 2.7 30 93.4 0.15 4 3 20419 19676 6 56.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.8 94.8 0.47 1.2 3.2 1938
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 PDB ENTRY 1VDC 2.8 20 16736 912 96.57 0.22625 0.22581 0.226 0.23431 0.2379 RANDOM 22.656
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] 1.91 3.25 -0.31 1.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.772 r_dihedral_angle_4_deg 20.419 r_dihedral_angle_3_deg 20.052 r_dihedral_angle_1_deg 13.505 r_scangle_it 1.448 r_angle_refined_deg 1.223 r_scbond_it 0.885 r_mcangle_it 0.732 r_mcbond_it 0.47 r_nbtor_refined 0.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.772 r_dihedral_angle_4_deg 20.419 r_dihedral_angle_3_deg 20.052 r_dihedral_angle_1_deg 13.505 r_scangle_it 1.448 r_angle_refined_deg 1.223 r_scbond_it 0.885 r_mcangle_it 0.732 r_mcbond_it 0.47 r_nbtor_refined 0.312 r_nbd_refined 0.225 r_xyhbond_nbd_refined 0.17 r_symmetry_vdw_refined 0.125 r_chiral_restr 0.089 r_bond_refined_d 0.009 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4786 Nucleic Acid Atoms Solvent Atoms 100 Heterogen Atoms 130
Software Software Software Name Purpose REFMAC refinement MAR345dtb data collection AUTOMAR data reduction SCALA data scaling MOLREP phasing