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Legionella monocytogenes SodA wt
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 chloride, 0.1 M Sodium acetate pH 5.0, 20% w/v PEG 6000
Crystal Properties Matthews coefficient Solvent content 2.59 52.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.72 α = 90 b = 94.09 β = 90 c = 94.52 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) 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 1.65 52.72 99.7 0.971 7 11.4 57150
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 1.65 1.68 0.541 10.5
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 1.65 47.26 57060 2869 99.571 0.217 0.2148 0.2148 0.2586 0.2588 24.456
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] 0.657 -0.281 -0.375
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.322 r_dihedral_angle_3_deg 15.401 r_dihedral_angle_6_deg 14.039 r_dihedral_angle_1_deg 12.36 r_lrange_it 6.388 r_lrange_other 6.388 r_scangle_it 5.758 r_scangle_other 5.756 r_scbond_it 4.195 r_scbond_other 4.194
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.322 r_dihedral_angle_3_deg 15.401 r_dihedral_angle_6_deg 14.039 r_dihedral_angle_1_deg 12.36 r_lrange_it 6.388 r_lrange_other 6.388 r_scangle_it 5.758 r_scangle_other 5.756 r_scbond_it 4.195 r_scbond_other 4.194 r_mcangle_it 3.487 r_mcangle_other 3.487 r_mcbond_it 2.811 r_mcbond_other 2.811 r_angle_refined_deg 2.011 r_angle_other_deg 0.889 r_chiral_restr_other 0.395 r_symmetry_xyhbond_nbd_refined 0.379 r_symmetry_nbd_refined 0.323 r_nbd_refined 0.248 r_symmetry_nbd_other 0.19 r_nbtor_refined 0.189 r_nbd_other 0.179 r_xyhbond_nbd_refined 0.15 r_chiral_restr 0.115 r_symmetry_nbtor_other 0.086 r_ncsr_local_group_1 0.082 r_metal_ion_refined 0.058 r_bond_refined_d 0.014 r_gen_planes_refined 0.014 r_bond_other_d 0.005 r_gen_planes_other 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3190 Nucleic Acid Atoms Solvent Atoms 398 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PHASER phasing Coot model building BUCCANEER model building