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X-ray structure of PmSOD2, superoxide dismutase from Perkinsus marinus
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8.5 298 0.17M Sodium Acetate trihydrate, 0.085M Tris Hydrochloride at pH 8.5, 25.5% w/v PEG 4000 and 15% glycerol, VAPOR DIFFUSION, temperature 298K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.43 α = 90 b = 73.894 β = 90 c = 94.53 γ = 90
Symmetry Space Group P 21 21 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 IMAGE PLATE MARRESEARCH M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.5 29.5 96.7 0.086 20 8 17174 2 2
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) 2.5 2.57 92.9 0.33 2.6 3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.5 29.21 14180 733 96.69 0.18549 0.18185 0.1824 0.25712 0.2548 RANDOM 15.739
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] -0.13 0.02 0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.519 r_dihedral_angle_4_deg 19.185 r_dihedral_angle_3_deg 18.71 r_dihedral_angle_1_deg 5.623 r_scangle_it 2.509 r_scbond_it 1.61 r_angle_refined_deg 1.408 r_mcangle_it 1.178 r_mcbond_it 0.693 r_nbtor_refined 0.315
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.519 r_dihedral_angle_4_deg 19.185 r_dihedral_angle_3_deg 18.71 r_dihedral_angle_1_deg 5.623 r_scangle_it 2.509 r_scbond_it 1.61 r_angle_refined_deg 1.408 r_mcangle_it 1.178 r_mcbond_it 0.693 r_nbtor_refined 0.315 r_symmetry_hbond_refined 0.263 r_symmetry_vdw_refined 0.247 r_nbd_refined 0.234 r_xyhbond_nbd_refined 0.188 r_chiral_restr 0.094 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3209 Nucleic Acid Atoms Solvent Atoms 202 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement MAR345 data collection SCALEPACK data scaling AMoRE phasing