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Crystal structure of human extracellular copper-zinc superoxide dismutase.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2C9V PDB ENTRY 2C9V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 PEG3350, THIOCYANATE, BIS-TRIS PROPANE PH 7.5
Crystal Properties Matthews coefficient Solvent content 1.93 36.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.738 α = 90 b = 93.588 β = 106.23 c = 75.6 γ = 90
Symmetry Space Group P 1 21 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 MARRESEARCH MIRRORS 2007-09-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX10.1 SRS PX10.1
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 28.2 97.3 0.06 16 3.7 81056 20.8
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 1.7 1.76 80 0.3 3 2.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 2C9V 1.7 28.2 76936 4057 97.2 0.152 0.15 0.1629 0.185 0.193 RANDOM 24.02
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] -1.24 -0.56 1.29 -0.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.6 r_dihedral_angle_4_deg 16.287 r_dihedral_angle_3_deg 11.711 r_dihedral_angle_1_deg 6.837 r_scangle_it 3.834 r_scbond_it 2.475 r_angle_refined_deg 1.71 r_mcangle_it 1.667 r_mcbond_it 1.01 r_angle_other_deg 0.996
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.6 r_dihedral_angle_4_deg 16.287 r_dihedral_angle_3_deg 11.711 r_dihedral_angle_1_deg 6.837 r_scangle_it 3.834 r_scbond_it 2.475 r_angle_refined_deg 1.71 r_mcangle_it 1.667 r_mcbond_it 1.01 r_angle_other_deg 0.996 r_symmetry_vdw_other 0.312 r_nbd_refined 0.262 r_nbd_other 0.228 r_xyhbond_nbd_refined 0.198 r_nbtor_refined 0.169 r_symmetry_hbond_refined 0.168 r_symmetry_vdw_refined 0.134 r_chiral_restr 0.114 r_nbtor_other 0.086 r_bond_refined_d 0.018 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4954 Nucleic Acid Atoms Solvent Atoms 889 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing