9J1G | pdb_00009j1g

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelAlphaFold 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION293.15Sodium malonate, 0.1 M HEPES (pH 7.0), and Jeffamine ED-2001
Crystal Properties
Matthews coefficientSolvent content
2.2745.88

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 108.386α = 90
b = 108.386β = 90
c = 44.628γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELRIGAKU HyPix-6000HE2022-08-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.54

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
11.527.1299.20.215.72.8748160
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.51.5399.71.3752.2

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-VALUE1.527.11148144238599.9610.120.11790.1160.16270.162414.354
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]
-0.531-0.265-0.5311.721
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg16.516
r_dihedral_angle_3_deg13.988
r_dihedral_angle_2_deg7.961
r_rigid_bond_restr7.197
r_lrange_it6.121
r_dihedral_angle_1_deg6.08
r_lrange_other5.382
r_scangle_it5.25
r_scangle_other5.249
r_scbond_other4.811
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg16.516
r_dihedral_angle_3_deg13.988
r_dihedral_angle_2_deg7.961
r_rigid_bond_restr7.197
r_lrange_it6.121
r_dihedral_angle_1_deg6.08
r_lrange_other5.382
r_scangle_it5.25
r_scangle_other5.249
r_scbond_other4.811
r_scbond_it4.808
r_mcangle_other2.912
r_mcangle_it2.886
r_mcbond_it2.228
r_mcbond_other2.228
r_angle_refined_deg1.557
r_angle_other_deg0.525
r_symmetry_nbd_refined0.246
r_nbd_refined0.228
r_symmetry_xyhbond_nbd_refined0.211
r_symmetry_nbd_other0.184
r_nbtor_refined0.181
r_xyhbond_nbd_refined0.181
r_nbd_other0.174
r_chiral_restr0.083
r_symmetry_nbtor_other0.077
r_bond_refined_d0.009
r_gen_planes_refined0.008
r_symmetry_xyhbond_nbd_other0.006
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2295
Nucleic Acid Atoms
Solvent Atoms315
Heterogen Atoms60

Software

Software
Software NamePurpose
REFMACrefinement
CrysalisProdata reduction
CrysalisProdata scaling
MOLREPphasing