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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 1ERT pdb entry 1ERT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 32% PEG 1500, 50 mM sodium phosphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.9 35.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.86 α = 90 b = 26.24 β = 95.02 c = 51.3 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 IMAGE PLATE RIGAKU RAXIS IV osmic mirrors 2006-04-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300
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 1.7 22.3 98 0.04 20.8 3.9 9820 9820 34.3
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) 1.7 1.76 94 0.19 4.2 3.1 991
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 (All) 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 1ERT 1.7 23 9319 9319 499 98.01 0.21024 0.21024 0.20876 0.2146 0.23908 0.2365 RANDOM 17.88
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 -0.22 1.15 -1.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.97 r_dihedral_angle_3_deg 15.429 r_dihedral_angle_1_deg 6.075 r_scangle_it 3.434 r_scbond_it 2.397 r_angle_refined_deg 2.011 r_mcangle_it 1.476 r_mcbond_it 1.27 r_angle_other_deg 1.165 r_symmetry_vdw_refined 0.545
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.97 r_dihedral_angle_3_deg 15.429 r_dihedral_angle_1_deg 6.075 r_scangle_it 3.434 r_scbond_it 2.397 r_angle_refined_deg 2.011 r_mcangle_it 1.476 r_mcbond_it 1.27 r_angle_other_deg 1.165 r_symmetry_vdw_refined 0.545 r_symmetry_hbond_refined 0.289 r_mcbond_other 0.262 r_nbd_refined 0.219 r_xyhbond_nbd_refined 0.194 r_symmetry_vdw_other 0.193 r_nbd_other 0.177 r_nbtor_refined 0.169 r_chiral_restr 0.112 r_nbtor_other 0.083 r_bond_refined_d 0.019 r_gen_planes_refined 0.007 r_gen_planes_other 0.004 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 928 Nucleic Acid Atoms Solvent Atoms 80 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection CrystalClear data reduction CrystalClear data scaling