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Crystal Structure of Deinococcus Radiodurans Thioredoxin Reductase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2A87 PDB ENTRY 2A87 CHAIN B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.1 293 35% PEG 4000, 0.2M ammonium acetate, citric acid buffer, VAPOR DIFFUSION, SITTING DROP, temperature 293K, pH 5.10
Crystal Properties Matthews coefficient Solvent content 2.32 47.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.994 α = 90 b = 83.994 β = 90 c = 160.11 γ = 120
Symmetry Space Group P 32 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 100 CCD ADSC QUANTUM 315 2005-08-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 8-BM APS 8-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.9 80.06 93.6 0.069 0.028 21.6 6.4 49077
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.9 2 93.6 0.332 0.332 21.6 6.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2A87 CHAIN B 1.9 19.36 49077 46481 2476 93.7 0.191 0.188 0.24 0.2373 RANDOM 21.96
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] -0.01 -0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.813 r_dihedral_angle_4_deg 21.509 r_dihedral_angle_3_deg 16.433 r_dihedral_angle_1_deg 9.414 r_scangle_it 4.108 r_scbond_it 2.614 r_angle_refined_deg 1.715 r_mcangle_it 1.553 r_mcbond_it 1.027 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.813 r_dihedral_angle_4_deg 21.509 r_dihedral_angle_3_deg 16.433 r_dihedral_angle_1_deg 9.414 r_scangle_it 4.108 r_scbond_it 2.614 r_angle_refined_deg 1.715 r_mcangle_it 1.553 r_mcbond_it 1.027 r_nbtor_refined 0.308 r_symmetry_vdw_refined 0.223 r_nbd_refined 0.217 r_symmetry_hbond_refined 0.21 r_chiral_restr 0.168 r_xyhbond_nbd_refined 0.159 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 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_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 4728 Nucleic Acid Atoms Solvent Atoms 521 Heterogen Atoms 106
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MrBUMP phasing