9J5A | pdb_00009j5a

ESTS1 phthalate ester degrading esterase from Sulfobacillus acidophilus in complex with p-nitrophenol


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
2.2545.55

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 108.156α = 90
b = 108.156β = 90
c = 44.549γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELRIGAKU HyPix-6000HE2022-09-29MSINGLE 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
11.525.981000.1314.73.1947847
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)
11.51.5399.411.3

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-VALUE1.523.42747831236599.9390.1280.12570.12560.17660.176814.289
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]
-0.098-0.049-0.0980.319
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg17.031
r_dihedral_angle_3_deg14.554
r_mcangle_it7.451
r_mcangle_other7.448
r_mcbond_it7.32
r_mcbond_other7.317
r_scangle_it7.055
r_scangle_other7.054
r_dihedral_angle_2_deg6.764
r_lrange_it6.394
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg17.031
r_dihedral_angle_3_deg14.554
r_mcangle_it7.451
r_mcangle_other7.448
r_mcbond_it7.32
r_mcbond_other7.317
r_scangle_it7.055
r_scangle_other7.054
r_dihedral_angle_2_deg6.764
r_lrange_it6.394
r_lrange_other6.261
r_dihedral_angle_1_deg6.239
r_scbond_it5.171
r_scbond_other5.17
r_rigid_bond_restr3.725
r_angle_refined_deg1.392
r_angle_other_deg0.498
r_nbd_refined0.226
r_symmetry_xyhbond_nbd_refined0.22
r_symmetry_nbd_other0.187
r_symmetry_nbd_refined0.187
r_nbtor_refined0.18
r_nbd_other0.172
r_xyhbond_nbd_refined0.152
r_symmetry_nbtor_other0.077
r_chiral_restr0.076
r_bond_refined_d0.008
r_gen_planes_refined0.008
r_bond_other_d0.005
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2312
Nucleic Acid Atoms
Solvent Atoms206
Heterogen Atoms103

Software

Software
Software NamePurpose
REFMACrefinement
CrysalisProdata reduction
CrysalisProdata scaling
MOLREPphasing