5XH2

Crystal structure of a novel PET hydrolase R103G/S131A mutant in complex with pNP 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 DROP7.5298Ammonium Sulfate, NaCl, HEPES
Crystal Properties
Matthews coefficientSolvent content
2.0239.02

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.784α = 90
b = 51.532β = 90
c = 84.373γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300-HS2017-04-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE TPS 05A0.9998NSRRCTPS 05A

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
11.22599.80.050.0530.01910869716
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)
11.21.2498.90.2120.2280.0810.9827.6

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 REPLACEMENTTHROUGHOUT4WFI1.22566256339199.590.09970.09840.1246RANDOM10.757
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]
-0.30.290.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.729
r_sphericity_free26.525
r_dihedral_angle_4_deg17.151
r_dihedral_angle_3_deg10.441
r_sphericity_bonded9.793
r_rigid_bond_restr7.103
r_dihedral_angle_1_deg6.596
r_angle_refined_deg1.489
r_angle_other_deg0.821
r_chiral_restr0.106
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.729
r_sphericity_free26.525
r_dihedral_angle_4_deg17.151
r_dihedral_angle_3_deg10.441
r_sphericity_bonded9.793
r_rigid_bond_restr7.103
r_dihedral_angle_1_deg6.596
r_angle_refined_deg1.489
r_angle_other_deg0.821
r_chiral_restr0.106
r_gen_planes_refined0.014
r_bond_refined_d0.011
r_gen_planes_other0.003
r_bond_other_d
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1912
Nucleic Acid Atoms
Solvent Atoms365
Heterogen Atoms30

Software

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