8W98 | pdb_00008w98

ESTS1 phthalate ester degrading esterase from Sulfobacillus acidophilus in complex with monoethylhexyl phtahalate and 2-ethylhexanol


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelAlphaFold 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION7293Sodium Malonate, HEPES pH 7, Jeffamine ED-2001
Crystal Properties
Matthews coefficientSolvent content
2.25717345.54092

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 108.004α = 90
b = 108.004β = 90
c = 44.662γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELRIGAKU HyPix-6000HE2023-08-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.925.9551000.19110.53.0139498
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.91.940.8141.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)Mean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE1.925.95523664116499.7720.1860.18420.18380.21720.217728.122
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]
-0.004-0.002-0.0040.014
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg16.376
r_dihedral_angle_3_deg15.599
r_dihedral_angle_2_deg14.521
r_dihedral_angle_1_deg6.455
r_lrange_it6.274
r_lrange_other6.238
r_scangle_it4.702
r_scangle_other4.701
r_scbond_it3.042
r_scbond_other3.041
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg16.376
r_dihedral_angle_3_deg15.599
r_dihedral_angle_2_deg14.521
r_dihedral_angle_1_deg6.455
r_lrange_it6.274
r_lrange_other6.238
r_scangle_it4.702
r_scangle_other4.701
r_scbond_it3.042
r_scbond_other3.041
r_mcangle_it2.859
r_mcangle_other2.859
r_mcbond_it1.968
r_mcbond_other1.968
r_angle_refined_deg1.319
r_angle_other_deg0.872
r_nbd_other0.276
r_nbd_refined0.225
r_symmetry_nbd_other0.202
r_symmetry_nbd_refined0.2
r_nbtor_refined0.181
r_xyhbond_nbd_refined0.176
r_symmetry_xyhbond_nbd_refined0.141
r_symmetry_nbtor_other0.081
r_chiral_restr0.061
r_bond_other_d0.038
r_bond_refined_d0.007
r_gen_planes_refined0.007
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2295
Nucleic Acid Atoms
Solvent Atoms70
Heterogen Atoms32

Software

Software
Software NamePurpose
REFMACrefinement
CrysalisProdata reduction
CrysalisProdata scaling
MOLREPphasing