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Crystal structure of S-nitroso thioredoxin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HXK PDB entry 2HXK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 32% PEG 4000, 50 mM sodium phosphate, ethanol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.8 31.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.08 α = 90 b = 25.749 β = 97.97 c = 85.86 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 100 CCD ADSC QUANTUM 315 bent Si-mirror 2006-04-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-C APS 14-BM-C
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 1.2 25.1 97.1 0.07 9.1 5.1 79717 79717 16.5
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) 1.2 1.24 98.4 0.24 3.3 4.8 7774
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT PDB entry 2HXK 1.2 25.13 73521 73521 3882 97.1 0.17859 0.17716 0.1858 0.20565 0.2112 RANDOM 13.78
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] -0.39 -0.03 0.25 0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.516 r_dihedral_angle_3_deg 14.112 r_sphericity_free 11.053 r_dihedral_angle_1_deg 6.275 r_sphericity_bonded 5.508 r_scangle_it 5.499 r_scbond_it 4.278 r_mcangle_it 3.07 r_rigid_bond_restr 2.655 r_mcbond_it 2.548
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.516 r_dihedral_angle_3_deg 14.112 r_sphericity_free 11.053 r_dihedral_angle_1_deg 6.275 r_sphericity_bonded 5.508 r_scangle_it 5.499 r_scbond_it 4.278 r_mcangle_it 3.07 r_rigid_bond_restr 2.655 r_mcbond_it 2.548 r_angle_refined_deg 1.96 r_mcbond_other 1.374 r_angle_other_deg 0.998 r_symmetry_vdw_refined 0.335 r_nbd_refined 0.276 r_symmetry_vdw_other 0.249 r_nbd_other 0.192 r_nbtor_refined 0.189 r_xyhbond_nbd_refined 0.14 r_symmetry_hbond_refined 0.13 r_nbtor_other 0.109 r_chiral_restr 0.103 r_bond_refined_d 0.02 r_gen_planes_refined 0.009 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2685 Nucleic Acid Atoms Solvent Atoms 115 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDISPLAYF data collection CrystalClear data reduction CrystalClear data scaling