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Structure of a thioredoxin reductase from Gloeobacter violaceus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Q7V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 30 & PEG-400
0.1 M Natrium Acetate, pH 4.5
0.2 M Calcium acetate
Crystal Properties Matthews coefficient Solvent content 2.56 51.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.278 α = 90 b = 122.042 β = 90 c = 139.153 γ = 90
Symmetry Space Group P 21 21 21
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 2M-F 2013-10-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.00004 SLS X06SA
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 1.9 49.222 100 0.06825 1 24.02 13.3 112104
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.968 100 1.523 1.59 12.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2q7v 1.9 49.222 1.36 112064 5592 99.96 0.1779 0.1767 0.1833 0.2015 0.2071
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.714 f_angle_d 0.982 f_chiral_restr 0.059 f_bond_d 0.01 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8949 Nucleic Acid Atoms Solvent Atoms 633 Heterogen Atoms 240
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing