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Crystal Structure of Human Sulfiredoxin (Srx) in Complex with ADP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XW3 PDB ENTRY 1XW3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 293 MPD, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 7.50
Crystal Properties Matthews coefficient Solvent content 2.9 56.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.451 α = 90 b = 68.451 β = 90 c = 50.891 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 IMAGE PLATE RIGAKU CONFOCAL BLUE MAX-FLUX 2004-07-09 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 2 29.64 99.6 0.051 30.9 9.63 9562
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2 2.07 95.3 4.4 5.03
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 1XW3 2 29.6 9602 9084 456 99.43 0.22068 0.21825 0.2202 0.27084 0.2696 RANDOM 27.872
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] 0.54 0.27 0.54 -0.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.158 r_dihedral_angle_4_deg 14.855 r_dihedral_angle_3_deg 14.42 r_dihedral_angle_1_deg 6.479 r_scangle_it 4.357 r_scbond_it 2.778 r_mcangle_it 1.834 r_angle_refined_deg 1.828 r_mcbond_it 1.126 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.158 r_dihedral_angle_4_deg 14.855 r_dihedral_angle_3_deg 14.42 r_dihedral_angle_1_deg 6.479 r_scangle_it 4.357 r_scbond_it 2.778 r_mcangle_it 1.834 r_angle_refined_deg 1.828 r_mcbond_it 1.126 r_nbtor_refined 0.301 r_symmetry_vdw_refined 0.24 r_xyhbond_nbd_refined 0.224 r_nbd_refined 0.216 r_chiral_restr 0.115 r_symmetry_hbond_refined 0.108 r_bond_refined_d 0.02 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 840 Nucleic Acid Atoms Solvent Atoms 71 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement d*TREK data reduction CNS refinement CNS phasing d*TREK data scaling