9J57 | pdb_00009j57

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


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), Jeffamine ED-2001
Crystal Properties
Matthews coefficientSolvent content
2.25945.59

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 108.048α = 90
b = 108.048β = 90
c = 44.672γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELRIGAKU HyPix-6000HE2023-01-13MSINGLE 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
11.827.731000.0415.23.9327832
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)
11.81.8410012.4

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-VALUE1.823.40427816127699.9280.1250.12170.12170.18540.18519.131
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]
-0.15-0.075-0.150.486
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg15.601
r_dihedral_angle_6_deg15.528
r_dihedral_angle_2_deg10.318
r_lrange_it6.666
r_scangle_it6.516
r_scangle_other6.514
r_lrange_other6.462
r_dihedral_angle_1_deg6.082
r_scbond_it5.835
r_scbond_other5.833
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg15.601
r_dihedral_angle_6_deg15.528
r_dihedral_angle_2_deg10.318
r_lrange_it6.666
r_scangle_it6.516
r_scangle_other6.514
r_lrange_other6.462
r_dihedral_angle_1_deg6.082
r_scbond_it5.835
r_scbond_other5.833
r_mcangle_it3.943
r_mcangle_other3.943
r_rigid_bond_restr3.283
r_mcbond_it3.106
r_mcbond_other3.091
r_angle_refined_deg1.3
r_angle_other_deg0.445
r_symmetry_nbd_refined0.335
r_nbd_refined0.229
r_symmetry_nbd_other0.189
r_symmetry_xyhbond_nbd_refined0.188
r_nbd_other0.187
r_nbtor_refined0.179
r_xyhbond_nbd_refined0.154
r_symmetry_nbtor_other0.078
r_chiral_restr0.065
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2302
Nucleic Acid Atoms
Solvent Atoms151
Heterogen Atoms42

Software

Software
Software NamePurpose
REFMACrefinement
CrysalisProdata reduction
CrysalisProdata scaling
MOLREPphasing