9J59 | pdb_00009j59

ESTS1 phthalate ester degrading esterase from Sulfobacillus acidophilus


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
2.2545.44

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 108.057α = 90
b = 108.057β = 90
c = 44.542γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELRIGAKU HyPix-6000HE2022-07-29MSINGLE 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
11.5525.951000.1716.52.9347747
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)
11.551.581000.8171.1

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-VALUE1.5525.9547728235999.9480.1540.1510.14620.20550.202315.315
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]
-0.329-0.165-0.3291.069
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg16.101
r_dihedral_angle_3_deg15.894
r_dihedral_angle_2_deg10.137
r_dihedral_angle_1_deg6.04
r_lrange_it5.304
r_scangle_it5.276
r_scangle_other5.274
r_lrange_other5.224
r_rigid_bond_restr4.886
r_scbond_it4.453
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg16.101
r_dihedral_angle_3_deg15.894
r_dihedral_angle_2_deg10.137
r_dihedral_angle_1_deg6.04
r_lrange_it5.304
r_scangle_it5.276
r_scangle_other5.274
r_lrange_other5.224
r_rigid_bond_restr4.886
r_scbond_it4.453
r_scbond_other4.452
r_mcangle_other3.051
r_mcangle_it3.046
r_mcbond_it2.486
r_mcbond_other2.422
r_angle_refined_deg1.458
r_symmetry_xyhbond_nbd_refined0.5
r_angle_other_deg0.493
r_nbd_other0.291
r_symmetry_nbd_refined0.255
r_nbd_refined0.224
r_symmetry_nbd_other0.188
r_nbtor_refined0.179
r_xyhbond_nbd_refined0.152
r_symmetry_nbtor_other0.078
r_chiral_restr0.075
r_xyhbond_nbd_other0.009
r_bond_refined_d0.008
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2303
Nucleic Acid Atoms
Solvent Atoms213
Heterogen Atoms28

Software

Software
Software NamePurpose
REFMACrefinement
CrysalisProdata reduction
CrysalisProdata scaling
MOLREPphasing