8S7S | pdb_00008s7s

Vanillyl-alcohol dehydrogenase from Marinicaulis flavus: P151G mutant


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelAlphaFold 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1EVAPORATION293G4 condition of the morpheus crystal screen by Hampton Research
Crystal Properties
Matthews coefficientSolvent content
2.7154.65

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.804α = 90
b = 144.145β = 90
c = 289.452γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2023-03-31MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE MASSIF-10.967700ESRFMASSIF-1

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
12.564.61000.2020.2070.0430.99712.522.866056
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)
12.52.561003.2743.3460.6860.60523.6

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 REPLACEMENTTHROUGHOUT2.564.662822318299.980.194940.1920.19920.251730.254RANDOM56.371
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]
2.8-0.13-2.67
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.184
r_long_range_B_other10.367
r_long_range_B_refined10.365
r_scangle_other8.366
r_dihedral_angle_2_deg8.265
r_dihedral_angle_1_deg7.82
r_mcangle_it7.339
r_mcangle_other7.339
r_scbond_it5.725
r_scbond_other5.725
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.184
r_long_range_B_other10.367
r_long_range_B_refined10.365
r_scangle_other8.366
r_dihedral_angle_2_deg8.265
r_dihedral_angle_1_deg7.82
r_mcangle_it7.339
r_mcangle_other7.339
r_scbond_it5.725
r_scbond_other5.725
r_mcbond_it5.161
r_mcbond_other5.161
r_angle_refined_deg1.515
r_angle_other_deg0.506
r_chiral_restr0.07
r_bond_refined_d0.008
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
r_dihedral_angle_4_deg
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 Atoms12234
Nucleic Acid Atoms
Solvent Atoms242
Heterogen Atoms159

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing