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Legionella monocytogenes SodA mutant GL to VI
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2RCV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 0.2 M Ammonium sulfate, 30 % w/v PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.54 51.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.99 α = 90 b = 93.38 β = 90 c = 94.87 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 PIXEL DECTRIS PILATUS 6M 2021-11-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.89842 Diamond I03
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 1.4 51.99 100 0.07 0.076 0.029 1 16.7 13.2 91660
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.4 1.42 0.538 9.4
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.4 47.435 91574 4561 99.993 0.177 0.1761 0.176 0.1913 0.1914 19.042
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] 1.014 -0.086 -0.928
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.847 r_dihedral_angle_6_deg 14.993 r_dihedral_angle_3_deg 12.106 r_dihedral_angle_1_deg 6.238 r_lrange_other 5.006 r_lrange_it 4.999 r_scangle_it 4.048 r_scangle_other 4.047 r_scbond_it 2.77 r_scbond_other 2.769
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.847 r_dihedral_angle_6_deg 14.993 r_dihedral_angle_3_deg 12.106 r_dihedral_angle_1_deg 6.238 r_lrange_other 5.006 r_lrange_it 4.999 r_scangle_it 4.048 r_scangle_other 4.047 r_scbond_it 2.77 r_scbond_other 2.769 r_mcangle_other 2.216 r_mcangle_it 2.213 r_angle_refined_deg 1.778 r_mcbond_it 1.643 r_mcbond_other 1.63 r_angle_other_deg 0.685 r_symmetry_xyhbond_nbd_refined 0.251 r_nbd_refined 0.239 r_symmetry_nbd_refined 0.196 r_nbtor_refined 0.194 r_symmetry_nbd_other 0.183 r_nbd_other 0.175 r_xyhbond_nbd_refined 0.134 r_chiral_restr 0.125 r_ncsr_local_group_1 0.079 r_symmetry_nbtor_other 0.078 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 r_bond_other_d 0.004 r_gen_planes_other 0.001 r_symmetry_xyhbond_nbd_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3196 Nucleic Acid Atoms Solvent Atoms 459 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PHASER phasing Coot model building BUCCANEER model building