9L1R | pdb_00009l1r

Crystal structure of AnAE in apo form, a fungal GDSL-Acetylesterase with acetylcholinesterase-like activity from Aspergillus niger


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherSelenium crystal structure as the initial model

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.52882.0 M Ammonium sulfate, 0.1 M Tris(hydroxymethyl)aminomethane-HCl, pH 8.5
Crystal Properties
Matthews coefficientSolvent content
2.5651.89

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.957α = 90
b = 78.957β = 90
c = 91.867γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2023-05-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNFPSS BEAMLINE BL19U10.97853NFPSSBL19U1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim 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
11.568.3899.70.0950.10.0330.99713953854
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.51.58990.580.630.2380.8412.86.8

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.568.3851087273199.670.148710.147290.15040.174920.1773RANDOM16.588
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]
-0.13-0.07-0.130.44
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg12.701
r_dihedral_angle_2_deg6.204
r_dihedral_angle_1_deg6.185
r_long_range_B_refined4.949
r_long_range_B_other4.777
r_scangle_other4.312
r_scbond_it2.924
r_scbond_other2.923
r_mcangle_it1.757
r_mcangle_other1.757
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg12.701
r_dihedral_angle_2_deg6.204
r_dihedral_angle_1_deg6.185
r_long_range_B_refined4.949
r_long_range_B_other4.777
r_scangle_other4.312
r_scbond_it2.924
r_scbond_other2.923
r_mcangle_it1.757
r_mcangle_other1.757
r_angle_refined_deg1.726
r_mcbond_it1.275
r_mcbond_other1.273
r_angle_other_deg0.597
r_chiral_restr0.089
r_bond_refined_d0.013
r_gen_planes_refined0.012
r_bond_other_d0.001
r_gen_planes_other0.001
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2099
Nucleic Acid Atoms
Solvent Atoms259
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing