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Crystal structure of Citrus limon Cu-Zn superoxide dismutase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Q2L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 Magnesium chloride, Calcium chloride, Imidazole, MES, PEG500 MME, PEG20000
Crystal Properties Matthews coefficient Solvent content 1.99 38.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.111 α = 90 b = 74.554 β = 106.86 c = 61.686 γ = 90
Symmetry Space Group P 1 21 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 PIXEL DECTRIS PILATUS3 S 6M 2021-06-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.86 49.36 99.8 0.068 0.081 0.044 0.998 9.3 3.4 44510
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.86 1.9 99.9 0.436 0.52 0.28 0.862 3.3
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 2Q2L 1.86 49.36 42281 2210 99.8 0.17752 0.17296 0.1787 0.26598 0.2733 RANDOM 24.054
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] 0.42 1.03 -2.09 0.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.75 r_dihedral_angle_4_deg 17.091 r_dihedral_angle_3_deg 16.641 r_dihedral_angle_1_deg 8.821 r_rigid_bond_restr 8.568 r_long_range_B_refined 6.583 r_long_range_B_other 6.554 r_scangle_other 6.217 r_scbond_it 5.376 r_scbond_other 5.376
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.75 r_dihedral_angle_4_deg 17.091 r_dihedral_angle_3_deg 16.641 r_dihedral_angle_1_deg 8.821 r_rigid_bond_restr 8.568 r_long_range_B_refined 6.583 r_long_range_B_other 6.554 r_scangle_other 6.217 r_scbond_it 5.376 r_scbond_other 5.376 r_mcangle_it 4.885 r_mcangle_other 4.884 r_mcbond_it 4.089 r_mcbond_other 4.087 r_angle_other_deg 1.273 r_angle_refined_deg 1.252 r_chiral_restr 0.054 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4268 Nucleic Acid Atoms Solvent Atoms 177 Heterogen Atoms 9
Software Software Software Name Purpose Aimless data scaling XDS data reduction REFMAC refinement MOLREP phasing