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Legionella monocytogenes SodA wt
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3LIO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 0.1 M MES/imidazole pH 6.5, 10% w/v PEG 20000, 20% v/v PEG MME 550, 0.02 M of each additive alcohol: 1,6-hexanediol, 1-butanol, (RS)-1,2-propanediol, 2-propanol, 1,4-butanediol, 1,3-propanediol
Crystal Properties Matthews coefficient Solvent content 3.44 64.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.19 α = 90 b = 105.58 β = 90 c = 162.58 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 2022-02-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 1 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2 67.48 100 0.997 10 13.1 121479
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 2 2.03 0.443 13.3
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2 67.472 121391 6036 99.987 0.196 0.194 0.194 0.2273 0.2274 42.896
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] -1.941 -1.537 3.478
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.289 r_dihedral_angle_3_deg 15.531 r_dihedral_angle_6_deg 15.5 r_lrange_it 8.186 r_lrange_other 8.185 r_scangle_it 6.974 r_scangle_other 6.973 r_dihedral_angle_1_deg 6.24 r_scbond_it 4.767 r_scbond_other 4.767
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.289 r_dihedral_angle_3_deg 15.531 r_dihedral_angle_6_deg 15.5 r_lrange_it 8.186 r_lrange_other 8.185 r_scangle_it 6.974 r_scangle_other 6.973 r_dihedral_angle_1_deg 6.24 r_scbond_it 4.767 r_scbond_other 4.767 r_mcangle_it 4.433 r_mcangle_other 4.432 r_mcbond_it 3.426 r_mcbond_other 3.424 r_angle_refined_deg 1.353 r_angle_other_deg 0.482 r_symmetry_nbd_refined 0.273 r_nbd_refined 0.206 r_nbtor_refined 0.191 r_symmetry_nbd_other 0.184 r_nbd_other 0.169 r_xyhbond_nbd_refined 0.136 r_symmetry_xyhbond_nbd_refined 0.134 r_symmetry_nbtor_other 0.077 r_chiral_restr 0.067 r_ncsr_local_group_14 0.058 r_ncsr_local_group_5 0.056 r_ncsr_local_group_15 0.051 r_ncsr_local_group_9 0.05 r_ncsr_local_group_3 0.047 r_ncsr_local_group_7 0.045 r_ncsr_local_group_10 0.045 r_ncsr_local_group_12 0.045 r_ncsr_local_group_2 0.043 r_ncsr_local_group_4 0.041 r_ncsr_local_group_13 0.041 r_ncsr_local_group_1 0.04 r_ncsr_local_group_6 0.038 r_ncsr_local_group_11 0.036 r_ncsr_local_group_8 0.035 r_symmetry_xyhbond_nbd_other 0.01 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9228 Nucleic Acid Atoms Solvent Atoms 585 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PHASER phasing Coot model building BUCCANEER model building