8SO5

Crystal structure of the engineered quorum quenching acylase MacQ variant M1 - acylated form


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4YF9 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP291100 mM Tris-HCl, 100 mM calcium acetate, 14-18% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.3647.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 97.07α = 90
b = 80.65β = 90.81
c = 101.6γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2022-12-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-D1.0332APS23-ID-D

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
12.3553.1698.90.99411.763.164842
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.352.4599.30.811

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 REPLACEMENTTHROUGHOUT2.3553.1661599324398.850.187340.185210.22811RANDOM28.977
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]
-0.04-0.010.010.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg13.87
r_long_range_B_refined6.521
r_long_range_B_other6.515
r_dihedral_angle_1_deg5.709
r_dihedral_angle_2_deg4.987
r_scangle_other4.368
r_mcangle_it3.485
r_mcangle_other3.485
r_scbond_it2.702
r_scbond_other2.702
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg13.87
r_long_range_B_refined6.521
r_long_range_B_other6.515
r_dihedral_angle_1_deg5.709
r_dihedral_angle_2_deg4.987
r_scangle_other4.368
r_mcangle_it3.485
r_mcangle_other3.485
r_scbond_it2.702
r_scbond_other2.702
r_mcbond_it2.241
r_mcbond_other2.241
r_angle_refined_deg0.561
r_angle_other_deg0.196
r_chiral_restr0.029
r_gen_planes_refined0.002
r_bond_refined_d0.001
r_bond_other_d
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11369
Nucleic Acid Atoms
Solvent Atoms572
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing