8S7N | pdb_00008s7n

Vanillyl-alcohol dehydrogenase from Marinicaulis flavus: P151L mutant bound to eugenol


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelAlphaFold 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION6.5293Condition C4 of the Morpheus screen (Hampton research)
Crystal Properties
Matthews coefficientSolvent content
3.7567.23

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 139.019α = 90
b = 139.019β = 90
c = 181.059γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2023-01-31MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA0.999990SLSX06SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
11.849.21000.1940.2010.0540.9981113.5163464
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.831003.7353.8821.0510.38813.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.849.2155094826299.960.158870.157540.16960.183970.1951RANDOM25.553
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]
0.560.56-1.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.607
r_dihedral_angle_4_deg19.499
r_dihedral_angle_3_deg13.075
r_dihedral_angle_1_deg7.111
r_long_range_B_refined6.061
r_long_range_B_other5.966
r_scangle_other4.981
r_scbond_it3.48
r_scbond_other3.479
r_mcangle_it2.657
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.607
r_dihedral_angle_4_deg19.499
r_dihedral_angle_3_deg13.075
r_dihedral_angle_1_deg7.111
r_long_range_B_refined6.061
r_long_range_B_other5.966
r_scangle_other4.981
r_scbond_it3.48
r_scbond_other3.479
r_mcangle_it2.657
r_mcangle_other2.656
r_mcbond_it2.047
r_mcbond_other2.047
r_angle_refined_deg1.705
r_angle_other_deg1.485
r_chiral_restr0.093
r_bond_refined_d0.013
r_gen_planes_refined0.011
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8174
Nucleic Acid Atoms
Solvent Atoms917
Heterogen Atoms239

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing