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Crystal structure of a thioredoxin reductase from Brucella melitensis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1CL0 PDB ENTRY 1CL0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 289 BrmeA.00058.a.A1 PS01310 at 21.1 mg/mL with 2 mM ebselen against Morpheus screen condition G1: 10% PEG20000, 20% PEG550 MME, 0.02 M sodium formate, 0.02 M ammonium acetate, 0.02 M trisodium citrate, 0.02 M sodium potassium L-tartrate, 0.02 M sodium oxamate, 0.1 M MES/imidazole, pH 6.5, crystal tracking ID 241371g1, unique puck ID qoj501, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.43 49.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.79 α = 90 b = 77.19 β = 90 c = 104.08 γ = 90
Symmetry Space Group P 2 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 CCD RAYONIX MX-300 2013-03-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.8 50 99.9 0.051 24.46 7.3 34300 34271 -3 29.839
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 1.8 1.85 99.9 0.481 4
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 1CL0 1.8 41.18 34224 1728 99.93 0.1639 0.1627 0.1731 0.1846 0.1912 RANDOM 25.1871
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] -0.88 0.77 0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.373 r_dihedral_angle_4_deg 17.32 r_dihedral_angle_3_deg 11.728 r_dihedral_angle_1_deg 5.611 r_mcangle_it 2.149 r_angle_refined_deg 1.483 r_mcbond_it 1.445 r_mcbond_other 1.414 r_angle_other_deg 0.768 r_chiral_restr 0.083
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.373 r_dihedral_angle_4_deg 17.32 r_dihedral_angle_3_deg 11.728 r_dihedral_angle_1_deg 5.611 r_mcangle_it 2.149 r_angle_refined_deg 1.483 r_mcbond_it 1.445 r_mcbond_other 1.414 r_angle_other_deg 0.768 r_chiral_restr 0.083 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2299 Nucleic Acid Atoms Solvent Atoms 233 Heterogen Atoms 54
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction