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Crystal structure of human apo Cu,Zn Superoxide Dismutase (SOD1)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1HL5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 289.1 0.1 M MES
20% PEG 3350, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 289.1K
Crystal Properties Matthews coefficient Solvent content 2.19 43.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 156.169 α = 90 b = 33.528 β = 111.64 c = 113.982 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 CCD OXFORD ONYX CCD Mirrors 2007-04-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE OXFORD DIFFRACTION ENHANCE ULTRA 1.54056
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 1.9 106 97.6 0.153 0.153 4.4 6.7 42832 42832 10.7
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) 1.9 2 92.9 0.409 0.409 4.1 5 5890
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 1HL5 1.9 39.01 38952 38952 3880 100 0.24308 0.24308 0.23948 0.2403 0.27909 0.2805 RANDOM 18.683
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] -1.44 -0.67 2.22 -1.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.373 r_dihedral_angle_4_deg 21.335 r_dihedral_angle_3_deg 19.496 r_dihedral_angle_1_deg 8.401 r_scangle_it 4.634 r_scbond_it 3.193 r_angle_refined_deg 2.412 r_mcangle_it 2.111 r_mcbond_it 1.363 r_nbtor_refined 0.321
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.373 r_dihedral_angle_4_deg 21.335 r_dihedral_angle_3_deg 19.496 r_dihedral_angle_1_deg 8.401 r_scangle_it 4.634 r_scbond_it 3.193 r_angle_refined_deg 2.412 r_mcangle_it 2.111 r_mcbond_it 1.363 r_nbtor_refined 0.321 r_nbd_refined 0.258 r_xyhbond_nbd_refined 0.239 r_symmetry_vdw_refined 0.199 r_symmetry_hbond_refined 0.164 r_chiral_restr 0.161 r_bond_refined_d 0.025 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4027 Nucleic Acid Atoms Solvent Atoms 299 Heterogen Atoms
Software Software Software Name Purpose CrysalisPro data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling