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Staphylococcus aureus lipase-Penfluridol complex (on the ground)
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 6.5 295 2.8M Sodium Formate, Acetate
Crystal Properties Matthews coefficient Solvent content 5.94 79.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.473 α = 90 b = 127.473 β = 90 c = 252.519 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 2023-06-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 0.9 SPring-8 BL41XU
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 2.23 50 99.8 0.998 12.4 13.1 192595
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 2.23 2.37 98.7 0.457 13
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 2.23 47 96088 5068 99.71 0.19166 0.1899 0.2022 0.22441 0.2335 RANDOM 78.31
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] -0.08 -0.08 0.15
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_other 37.358 r_long_range_B_refined 37.354 r_scangle_other 32.645 r_mcangle_it 26.128 r_mcangle_other 26.089 r_scbond_it 24.374 r_scbond_other 24.37 r_mcbond_it 19.631 r_mcbond_other 19.563 r_dihedral_angle_3_deg 19.482
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_other 37.358 r_long_range_B_refined 37.354 r_scangle_other 32.645 r_mcangle_it 26.128 r_mcangle_other 26.089 r_scbond_it 24.374 r_scbond_other 24.37 r_mcbond_it 19.631 r_mcbond_other 19.563 r_dihedral_angle_3_deg 19.482 r_dihedral_angle_2_deg 11.544 r_dihedral_angle_1_deg 6.402 r_rigid_bond_restr 5.005 r_angle_refined_deg 1.568 r_angle_other_deg 0.575 r_chiral_restr 0.091 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_dihedral_angle_4_deg 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_scangle_it r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6048 Nucleic Acid Atoms Solvent Atoms 46 Heterogen Atoms 234
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing