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Crystal structure of iron superoxide dismutase from Leishmania major
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ISA PDB ENTRY 1ISA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 289 EBS internal tracking number 232906f2, LemaA.01199.b.A2_PW34974 at 35.33 mg/mL in 25 mM HEPES, pH 7.0, 500 mM sodium chloride, 2 mM DTT, 0.025% sodium azide, 5% glycerol, 0.4 uL + 0.4 uL drop with 18.4% PEG3350, 184 mM potassium formate, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.57 52.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.03 α = 91.66 b = 102.74 β = 96.36 c = 168.24 γ = 95.01
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 2012-04-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.3 0.976484 ALS 5.0.3
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 1.85 19.774 96.2 0.046 17.65 256038 -3 31.63
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 1.85 1.9 91.5 0.418 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 1ISA 1.85 19.774 256038 12890 0.175 0.173 0.1752 0.203 0.2043 RANDOM 28.83
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] 1.6 -0.02 -2.07 -1.4 -0.12 -0.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.961 r_dihedral_angle_4_deg 14.85 r_dihedral_angle_3_deg 12.594 r_dihedral_angle_1_deg 5.805 r_angle_refined_deg 1.283 r_chiral_restr 0.089 r_bond_refined_d 0.01 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 20026 Nucleic Acid Atoms Solvent Atoms 1422 Heterogen Atoms 12
Software Software Software Name Purpose PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling XDS data scaling