9GOV | pdb_00009gov

4-Allyl syringol oxidase from Streptomyces cavernae: complex with Propanol syringol


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelAlphaFold 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION7.52930.06 M of MgCl26 H2O, CaCl2 2 H2O, 0.1 M Tris, bicine, 20% glycerol, 10% PEG 4000
Crystal Properties
Matthews coefficientSolvent content
2.4349.28

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.993α = 90
b = 82.993β = 90
c = 297.577γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M-F2021-11-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DA0.965459SLSX06DA

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
1245.8899.40.0920.1070.0530.9968.8477465
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)
122.041000.810.9330.4590.5244

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 REPLACEMENTTHROUGHOUT245.8473450391599.40.185890.183620.18920.229210.224RANDOM35.887
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]
-0.23-0.12-0.230.75
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.757
r_dihedral_angle_4_deg18.954
r_dihedral_angle_3_deg16.39
r_long_range_B_refined8.117
r_long_range_B_other8.108
r_dihedral_angle_1_deg7.656
r_scangle_other5.118
r_mcangle_it4.078
r_mcangle_other4.078
r_scbond_it3.458
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.757
r_dihedral_angle_4_deg18.954
r_dihedral_angle_3_deg16.39
r_long_range_B_refined8.117
r_long_range_B_other8.108
r_dihedral_angle_1_deg7.656
r_scangle_other5.118
r_mcangle_it4.078
r_mcangle_other4.078
r_scbond_it3.458
r_scbond_other3.458
r_mcbond_it2.981
r_mcbond_other2.98
r_angle_refined_deg1.636
r_angle_other_deg1.314
r_chiral_restr0.079
r_bond_refined_d0.009
r_gen_planes_refined0.008
r_gen_planes_other0.002
r_bond_other_d0.001
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 Atoms8127
Nucleic Acid Atoms
Solvent Atoms576
Heterogen Atoms136

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing