9J5C | pdb_00009j5c

ESTS1 phthalate ester degrading esterase from Sulfobacillus acidophilus in complex with diethylhexyl 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
2.27846.049

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 108.258α = 90
b = 108.258β = 90
c = 44.872γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELRIGAKU HyPix-6000HE2023-01-14MSINGLE 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
12.725.6499.90.4315.53.068440
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)
12.72.8313.7

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-VALUE2.723.45843342499.8340.2180.2140.21460.29450.28585
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]
0.4050.2020.405-1.313
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg15.429
r_dihedral_angle_6_deg13.912
r_dihedral_angle_2_deg9.299
r_dihedral_angle_1_deg7.306
r_angle_refined_deg1.148
r_angle_other_deg0.369
r_nbd_refined0.216
r_symmetry_xyhbond_nbd_refined0.215
r_symmetry_nbd_other0.201
r_nbd_other0.184
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg15.429
r_dihedral_angle_6_deg13.912
r_dihedral_angle_2_deg9.299
r_dihedral_angle_1_deg7.306
r_angle_refined_deg1.148
r_angle_other_deg0.369
r_nbd_refined0.216
r_symmetry_xyhbond_nbd_refined0.215
r_symmetry_nbd_other0.201
r_nbd_other0.184
r_nbtor_refined0.179
r_xyhbond_nbd_refined0.179
r_symmetry_nbd_refined0.142
r_symmetry_nbtor_other0.081
r_chiral_restr0.052
r_symmetry_xyhbond_nbd_other0.028
r_rigid_bond_restr0.012
r_bond_refined_d0.005
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.002
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_lrange_it
r_lrange_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2287
Nucleic Acid Atoms
Solvent Atoms84
Heterogen Atoms56

Software

Software
Software NamePurpose
REFMACrefinement
CrysalisProdata reduction
CrysalisProdata scaling
MOLREPphasing