5XFY

Crystal structure of a novel PET hydrolase S131A mutant from Ideonella sakaiensis 201-F6


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5298Ammonium Sulfate, NaCl, Bis-Tris
Crystal Properties
Matthews coefficientSolvent content
2.1542.85

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 114.185α = 90
b = 50.331β = 92.24
c = 40.979γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-3002016-12-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE BL15A11.0NSRRCBL15A1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
11.42599.70.0360.040.01624.95.745597
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)
11.41.451000.2070.2280.0940.9775.84562

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-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4WFI1.42543291230699.590.13550.13440.1589RANDOM16.788
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]
-0.94-0.320.680.29
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.033
r_dihedral_angle_4_deg13.152
r_dihedral_angle_3_deg11.525
r_dihedral_angle_1_deg6.546
r_angle_refined_deg1.501
r_angle_other_deg0.778
r_chiral_restr0.102
r_gen_planes_refined0.015
r_bond_refined_d0.011
r_gen_planes_other0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.033
r_dihedral_angle_4_deg13.152
r_dihedral_angle_3_deg11.525
r_dihedral_angle_1_deg6.546
r_angle_refined_deg1.501
r_angle_other_deg0.778
r_chiral_restr0.102
r_gen_planes_refined0.015
r_bond_refined_d0.011
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1918
Nucleic Acid Atoms
Solvent Atoms190
Heterogen Atoms21

Software

Software
Software NamePurpose
HKL-2000data collection
HKL-2000data scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing
HKLdata reduction
HKLdata scaling