4YJI

The Crystal Structure of a Bacterial Aryl Acylamidase Belonging to the Amidase signature (AS) enzymes family


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4YJ6 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP295.151.2 M NaH2PO4/0.8 M K2HPO4, 0.1 M CAPS pH 10.5, 0.2 M Li2SO4 and 0.1 M ZnCl2
Crystal Properties
Matthews coefficientSolvent content
2.9157.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.98α = 90
b = 75.98β = 90
c = 214.71γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2014-05-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPAL/PLS BEAMLINE 5C (4A)0.979PAL/PLS5C (4A)

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
11.7343.8498.611.526.965840

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTNONE4YJ61.7342.9763668193795.060.16720.16650.188
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d12.549
f_angle_d1.08
f_chiral_restr0.043
f_bond_d0.007
f_plane_restr0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3707
Nucleic Acid Atoms
Solvent Atoms545
Heterogen Atoms25

Software

Software
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
MOSFLMdata scaling
PHENIXphasing