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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, ethanol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.66 25.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.35 α = 90 b = 25.74 β = 98.2 c = 86.02 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 2006-03-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.5418
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 1.65 24.2 99 0.04 16.1 2.7 29229 29229 26
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) 1.65 1.71 99.9 0.14 3.6 2.2 3122
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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1ERT 1.65 24.2 29229 29229 1576 98.88 0.19714 0.19489 0.2017 0.23919 0.2408 RANDOM 13.156
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] -0.37 0.01 0.24 0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.805 r_dihedral_angle_3_deg 15.869 r_dihedral_angle_1_deg 5.877 r_scangle_it 4.1 r_scbond_it 2.988 r_angle_refined_deg 1.861 r_mcangle_it 1.82 r_mcbond_it 1.624 r_angle_other_deg 1.068 r_mcbond_other 0.384
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.805 r_dihedral_angle_3_deg 15.869 r_dihedral_angle_1_deg 5.877 r_scangle_it 4.1 r_scbond_it 2.988 r_angle_refined_deg 1.861 r_mcangle_it 1.82 r_mcbond_it 1.624 r_angle_other_deg 1.068 r_mcbond_other 0.384 r_symmetry_vdw_refined 0.297 r_xyhbond_nbd_refined 0.261 r_symmetry_vdw_other 0.245 r_nbd_refined 0.23 r_nbd_other 0.189 r_chiral_restr 0.181 r_nbtor_refined 0.175 r_symmetry_hbond_refined 0.153 r_nbtor_other 0.088 r_bond_refined_d 0.021 r_gen_planes_refined 0.008 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2741 Nucleic Acid Atoms Solvent Atoms 152 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection CrystalClear data reduction CrystalClear data scaling MOLREP phasing