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Staphylococcus aureus lipase S116A inactive mutant-PSA complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6KSI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.5 295 2.45M Sodium Formate, 0.1M Sodium Acetate pH4.5
Crystal Properties Matthews coefficient Solvent content 5.88 79.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 131.348 α = 90 b = 131.348 β = 90 c = 249.851 γ = 90
Symmetry Space Group P 41 2 2
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 EIGER X 16M 2023-02-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 2.02 50 99.9 0.08 0.999 12.96 7.09 272631
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.02 2.14 99.5 0.246 0.503 6.72
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.02 48 135329 7123 99.9 0.2189 0.21784 0.23905 0.2353 RANDOM 58.076
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] 1.73 1.73 -3.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.861 r_dihedral_angle_2_deg 12.199 r_long_range_B_refined 9.614 r_scbond_it 7.371 r_dihedral_angle_1_deg 6.188 r_mcangle_it 5.861 r_mcbond_it 4.575 r_angle_refined_deg 1.646 r_chiral_restr 0.149 r_bond_refined_d 0.008
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.861 r_dihedral_angle_2_deg 12.199 r_long_range_B_refined 9.614 r_scbond_it 7.371 r_dihedral_angle_1_deg 6.188 r_mcangle_it 5.861 r_mcbond_it 4.575 r_angle_refined_deg 1.646 r_chiral_restr 0.149 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_dihedral_angle_4_deg 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6046 Nucleic Acid Atoms Solvent Atoms 216 Heterogen Atoms 209
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing