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Staphylococcus aureus lipase -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 4.5 296 Sodium Formate, Acetate
Crystal Properties Matthews coefficient Solvent content 5.94 79.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 132.324 α = 90 b = 132.324 β = 90 c = 248.636 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 2.19 50 99.9 0.11 0.999 9.57 7.1 217650
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 2.19 2.32 99.6 0.427 6.69
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.19 48.16 108410 5706 99.94 0.19936 0.19837 0.1993 0.21806 0.2187 RANDOM 61.962
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] 1.36 1.36 -2.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.499 r_long_range_B_refined 10.87 r_dihedral_angle_2_deg 10.614 r_scbond_it 8.371 r_mcangle_it 6.705 r_dihedral_angle_1_deg 6.272 r_mcbond_it 5.188 r_angle_refined_deg 1.744 r_chiral_restr 0.153 r_bond_refined_d 0.008
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.499 r_long_range_B_refined 10.87 r_dihedral_angle_2_deg 10.614 r_scbond_it 8.371 r_mcangle_it 6.705 r_dihedral_angle_1_deg 6.272 r_mcbond_it 5.188 r_angle_refined_deg 1.744 r_chiral_restr 0.153 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 6048 Nucleic Acid Atoms Solvent Atoms 142 Heterogen Atoms 209
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing