9FFK | pdb_00009ffk

Vanillyl alcohol oxidase from Novosphingobium sp in complex with vanillyl alcohol


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelAlphaFold 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293.15Morpheus H2
Crystal Properties
Matthews coefficientSolvent content
2.5752.15

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.845α = 90
b = 96.766β = 90
c = 129.111γ = 90
Symmetry
Space GroupP 2 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER R 4M2023-04-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE MASSIF-30.999870ESRFMASSIF-3

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
11.7129.1199.70.1620.1670.0370.99910.120125029
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)
11.71.7399.72.4662.5350.5840.70718.6

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 REPLACEMENTTHROUGHOUT1.790.85118543619899.480.224260.222740.23330.25350.2642RANDOM25.38
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]
-0.14-1.621.76
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.694
r_dihedral_angle_4_deg19.286
r_dihedral_angle_3_deg13.56
r_dihedral_angle_1_deg7.072
r_long_range_B_refined6.027
r_long_range_B_other6
r_scangle_other4.693
r_mcangle_it3.25
r_mcangle_other3.25
r_scbond_it3.212
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.694
r_dihedral_angle_4_deg19.286
r_dihedral_angle_3_deg13.56
r_dihedral_angle_1_deg7.072
r_long_range_B_refined6.027
r_long_range_B_other6
r_scangle_other4.693
r_mcangle_it3.25
r_mcangle_other3.25
r_scbond_it3.212
r_scbond_other3.212
r_mcbond_it2.329
r_mcbond_other2.329
r_angle_refined_deg1.735
r_angle_other_deg1.449
r_chiral_restr0.09
r_bond_refined_d0.012
r_gen_planes_refined0.011
r_bond_other_d0.002
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 Atoms7758
Nucleic Acid Atoms
Solvent Atoms558
Heterogen Atoms146

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing