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Crystal structure of Saccharomyces cerevisiae thioredoxin reductase 1 (Trr1)
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 VAPOR DIFFUSION, HANGING DROP 4 293 2.7 M Sodium citrate pH 4.0, 12% PEG 3000, 0.1 M Trimethylamine hydrochloride. Drop volume of 6.0 ml, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.39 48.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.975 α = 90 b = 135.411 β = 89.95 c = 75.819 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 CCD MAR CCD 165 mm mirrors 2004-11-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE D03B-MX1 1.431 LNLS D03B-MX1
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 2.4 50 97.03 0.099 17.6 6.1 46488 4.3
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 2.4 2.462 99.3 0.32 4.4 6
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1VDC 2.4 50 46488 2459 97.03 0.17053 0.1693 0.1985 0.19356 RANDOM 20.636
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] -3.22 1.94 -1.35 4.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.28 r_dihedral_angle_4_deg 18.561 r_dihedral_angle_3_deg 17.859 r_dihedral_angle_1_deg 7.114 r_scangle_it 4.326 r_scbond_it 2.938 r_angle_refined_deg 2.253 r_mcangle_it 1.638 r_mcbond_it 0.993 r_chiral_restr 0.141
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.28 r_dihedral_angle_4_deg 18.561 r_dihedral_angle_3_deg 17.859 r_dihedral_angle_1_deg 7.114 r_scangle_it 4.326 r_scbond_it 2.938 r_angle_refined_deg 2.253 r_mcangle_it 1.638 r_mcbond_it 0.993 r_chiral_restr 0.141 r_bond_refined_d 0.024 r_gen_planes_refined 0.011 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined 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 9262 Nucleic Acid Atoms Solvent Atoms 277 Heterogen Atoms 290
Software Software Software Name Purpose MAR345dtb data collection AMoRE phasing REFMAC refinement MOSFLM data reduction SCALA data scaling