9J5B | pdb_00009j5b

ESTS1 phthalate ester degrading esterase from Sulfobacillus acidophilus in complex with Dimethyl phthalate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelAlphaFold 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION7293.15Sodium malonate, 0.1 M HEPES (pH 7.0), Jeffamine ED-2001
Crystal Properties
Matthews coefficientSolvent content
2.23444.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 107.668α = 90
b = 107.668β = 90
c = 44.489γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELRIGAKU HyPix-6000HE2022-10-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.54

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim 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
11.625.481000.1812.43.2847379
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.61.6310011.2

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-VALUE1.625.4839076184899.9590.150.14750.18420.1940.22468.656
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]
-0.047-0.024-0.0470.153
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg17.785
r_dihedral_angle_6_deg16.231
r_dihedral_angle_3_deg14.646
r_dihedral_angle_1_deg6.167
r_rigid_bond_restr3.637
r_lrange_other2.831
r_lrange_it2.822
r_scangle_it2.725
r_scangle_other2.724
r_scbond_it2.358
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg17.785
r_dihedral_angle_6_deg16.231
r_dihedral_angle_3_deg14.646
r_dihedral_angle_1_deg6.167
r_rigid_bond_restr3.637
r_lrange_other2.831
r_lrange_it2.822
r_scangle_it2.725
r_scangle_other2.724
r_scbond_it2.358
r_scbond_other2.357
r_mcangle_other1.711
r_mcangle_it1.701
r_angle_refined_deg1.442
r_mcbond_it1.335
r_mcbond_other1.335
r_angle_other_deg0.489
r_symmetry_nbd_refined0.237
r_nbd_other0.228
r_nbd_refined0.222
r_symmetry_xyhbond_nbd_refined0.214
r_symmetry_nbd_other0.189
r_nbtor_refined0.181
r_xyhbond_nbd_refined0.171
r_symmetry_nbtor_other0.081
r_chiral_restr0.074
r_bond_refined_d0.008
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2313
Nucleic Acid Atoms
Solvent Atoms162
Heterogen Atoms91

Software

Software
Software NamePurpose
REFMACrefinement
CrysalisProdata reduction
CrysalisProdata scaling
MOLREPphasing