8K7Q

Staphylococcus aureus lipase S116A inactive mutant-PSA complex


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6KSI 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.52952.45M Sodium Formate, 0.1M Sodium Acetate pH4.5
Crystal Properties
Matthews coefficientSolvent content
5.8879.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 131.348α = 90
b = 131.348β = 90
c = 249.851γ = 90
Symmetry
Space GroupP 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2023-02-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL44XU0.9SPring-8BL44XU

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim I (All)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.025099.90.080.99912.967.09272631
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.022.1499.50.2460.5036.72

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.0248135329712399.90.21890.217840.23905RANDOM58.076
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]
1.731.73-3.45
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg17.861
r_dihedral_angle_2_deg12.199
r_long_range_B_refined9.614
r_scbond_it7.371
r_dihedral_angle_1_deg6.188
r_mcangle_it5.861
r_mcbond_it4.575
r_angle_refined_deg1.646
r_chiral_restr0.149
r_bond_refined_d0.008
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg17.861
r_dihedral_angle_2_deg12.199
r_long_range_B_refined9.614
r_scbond_it7.371
r_dihedral_angle_1_deg6.188
r_mcangle_it5.861
r_mcbond_it4.575
r_angle_refined_deg1.646
r_chiral_restr0.149
r_bond_refined_d0.008
r_gen_planes_refined0.008
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 AtomsNumber
Protein Atoms6046
Nucleic Acid Atoms
Solvent Atoms216
Heterogen Atoms209

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing