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The crystal structure of Sod2 from Saccharomyces cerevisiae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KKC PDB ENTRY 1KKC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8.5 289 50% MPD, 0.2M NH4H2PO4,0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.76 55.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.74 α = 90 b = 92.74 β = 90 c = 92.74 γ = 90
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 MAR scanner 345 mm plate 2007-01-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
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 2.05 18.55 99.9 0.08 18.3 6.9 16963 2 22
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 2.05 2.16 100 0.376 5.2 6.7 2463
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 (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 PDB ENTRY 1KKC 2.05 15 16063 857 100 0.19666 0.19666 0.19476 0.1956 0.23357 0.2293 RANDOM 19.061
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.814 r_dihedral_angle_4_deg 34.559 r_dihedral_angle_3_deg 14.501 r_dihedral_angle_1_deg 5.153 r_scangle_it 1.613 r_scbond_it 1.008 r_angle_refined_deg 0.992 r_mcangle_it 0.702 r_mcbond_it 0.413 r_nbtor_refined 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.814 r_dihedral_angle_4_deg 34.559 r_dihedral_angle_3_deg 14.501 r_dihedral_angle_1_deg 5.153 r_scangle_it 1.613 r_scbond_it 1.008 r_angle_refined_deg 0.992 r_mcangle_it 0.702 r_mcbond_it 0.413 r_nbtor_refined 0.3 r_nbd_refined 0.175 r_symmetry_vdw_refined 0.153 r_symmetry_hbond_refined 0.113 r_xyhbond_nbd_refined 0.109 r_chiral_restr 0.07 r_bond_refined_d 0.007 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1609 Nucleic Acid Atoms Solvent Atoms 122 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement MAR345dtb data collection MOSFLM data reduction SCALA data scaling AMoRE phasing