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Crystal Structure of the Cu/Zn Superoxide Dismutase from Cryptococcus liquefaciens Strain N6
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1F1G PDB ENTRY 1F1G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 30% PEG 4000, 0.2M sodium acetate, 0.1M Tris-Cl , pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal Properties Matthews coefficient Solvent content 2.04 39.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.854 α = 90 b = 111.768 β = 90 c = 70.456 γ = 90
Symmetry Space Group C 2 2 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 ADSC QUANTUM 315 KB MIRRORS 2004-12-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.000 SPring-8 BL41XU
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 1.2 70.53 99.9 0.065 31.3 7 44741 44741
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 1.24 99.5 0.459 3.5 6.3 4372
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1F1G 1.2 50 44698 44698 2249 99.87 0.15 0.15 0.149 0.166 0.1639 RANDOM 10.769
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] -0.25 0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.231 r_dihedral_angle_4_deg 12.736 r_dihedral_angle_3_deg 9.205 r_sphericity_free 7.475 r_dihedral_angle_1_deg 6.395 r_sphericity_bonded 4.028 r_scangle_it 3.216 r_scbond_it 2.55 r_mcangle_it 2.163 r_rigid_bond_restr 1.706
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.231 r_dihedral_angle_4_deg 12.736 r_dihedral_angle_3_deg 9.205 r_sphericity_free 7.475 r_dihedral_angle_1_deg 6.395 r_sphericity_bonded 4.028 r_scangle_it 3.216 r_scbond_it 2.55 r_mcangle_it 2.163 r_rigid_bond_restr 1.706 r_mcbond_it 1.496 r_angle_refined_deg 1.362 r_nbtor_refined 0.309 r_symmetry_hbond_refined 0.249 r_nbd_refined 0.214 r_xyhbond_nbd_refined 0.177 r_symmetry_vdw_refined 0.161 r_chiral_restr 0.089 r_metal_ion_refined 0.044 r_bond_refined_d 0.01 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1078 Nucleic Acid Atoms Solvent Atoms 154 Heterogen Atoms 6
Software Software Software Name Purpose MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling