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Crystal structure of cisplatinated bovine Cu,Zn superoxide dismutase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SXS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 50mM Tris HCl, 18% PEG 4000, 20% 2-propanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.87 56.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.207 α = 90 b = 50.92 β = 90 c = 146.738 γ = 90
Symmetry Space Group P 21 21 21
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 OXFORD ONYX CCD Enhance ultra, graded multilayer 2005-06-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE OXFORD DIFFRACTION ENHANCED ULTRA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.8 147.44 96.1 0.17 0.17 4.1 4.8 32303 32303 5.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.9 81.4 0.42 0.42 1.7 2.2 3880
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 MOLECULAR REPLACEMENT THROUGHOUT 1SXS 1.8 44.9 29382 29382 2921 100 0.20545 0.20545 0.20243 0.2023 0.23601 0.2349 RANDOM 7.303
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] 0.71 -0.23 -0.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.997 r_dihedral_angle_4_deg 16.34 r_dihedral_angle_3_deg 13.557 r_dihedral_angle_1_deg 6.485 r_sphericity_free 6.117 r_scangle_it 3.437 r_scbond_it 2.222 r_angle_refined_deg 1.439 r_mcangle_it 1.146 r_mcbond_it 0.784
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.997 r_dihedral_angle_4_deg 16.34 r_dihedral_angle_3_deg 13.557 r_dihedral_angle_1_deg 6.485 r_sphericity_free 6.117 r_scangle_it 3.437 r_scbond_it 2.222 r_angle_refined_deg 1.439 r_mcangle_it 1.146 r_mcbond_it 0.784 r_nbtor_refined 0.298 r_nbd_refined 0.184 r_xyhbond_nbd_refined 0.159 r_symmetry_hbond_refined 0.155 r_symmetry_vdw_refined 0.132 r_chiral_restr 0.106 r_metal_ion_refined 0.071 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 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_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_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2184 Nucleic Acid Atoms Solvent Atoms 287 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling MOLREP phasing