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Crystal Structure of Human Sulfiredoxin (Srx)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other SEMET MODEL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 293 MPD, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 7.50
Crystal Properties Matthews coefficient Solvent content 2.9 56.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.057 α = 90 b = 68.057 β = 90 c = 51.302 γ = 120
Symmetry Space Group P 32 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 RIGAKU SATURN 92 CONFOCAL BLUE MAX-FLUX 2004-03-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007
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 38.7 98.9 0.039 27.1 7.22 16690
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 92.3 0.24 3.9 2.88
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 SEMET MODEL 1.65 38.69 16877 15839 845 98.89 0.21584 0.21372 0.2102 0.25817 0.2561 RANDOM 21.318
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] 0.05 0.03 0.05 -0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.876 r_dihedral_angle_4_deg 20.871 r_dihedral_angle_3_deg 14.328 r_dihedral_angle_1_deg 5.69 r_scangle_it 3.785 r_scbond_it 2.66 r_mcangle_it 1.713 r_angle_refined_deg 1.566 r_mcbond_it 1.087 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.876 r_dihedral_angle_4_deg 20.871 r_dihedral_angle_3_deg 14.328 r_dihedral_angle_1_deg 5.69 r_scangle_it 3.785 r_scbond_it 2.66 r_mcangle_it 1.713 r_angle_refined_deg 1.566 r_mcbond_it 1.087 r_nbtor_refined 0.308 r_symmetry_vdw_refined 0.22 r_nbd_refined 0.217 r_symmetry_hbond_refined 0.212 r_xyhbond_nbd_refined 0.12 r_chiral_restr 0.099 r_bond_refined_d 0.019 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 868 Nucleic Acid Atoms Solvent Atoms 112 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement d*TREK data reduction CNS refinement CNS phasing d*TREK data scaling