8RPG | pdb_00008rpg

Crystal structure of an alcohol oxidase from Streptomyces hiroshimensis


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelAlphaFold 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.5291.1530 % Polyethylene glycol 4000 100 mM TRIS pH 8.5 200 mM Magnesium chloride
Crystal Properties
Matthews coefficientSolvent content
2.4148.86

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.51α = 90
b = 97.688β = 90
c = 68.047γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2023-10-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALBA BEAMLINE XALOC0.979180ALBAXALOC

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
1297.691000.05715.44.636978
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.110.2355.3

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 REPLACEMENTTHROUGHOUT262.2135032189899.910.153170.151020.16460.193240.1994RANDOM24.456
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]
0.68-1.670.99
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg12.12
r_dihedral_angle_2_deg8.949
r_long_range_B_refined8.338
r_long_range_B_other7.508
r_dihedral_angle_1_deg6.689
r_scangle_other5.18
r_scbond_it3.455
r_scbond_other3.455
r_mcangle_other2.737
r_mcangle_it2.735
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg12.12
r_dihedral_angle_2_deg8.949
r_long_range_B_refined8.338
r_long_range_B_other7.508
r_dihedral_angle_1_deg6.689
r_scangle_other5.18
r_scbond_it3.455
r_scbond_other3.455
r_mcangle_other2.737
r_mcangle_it2.735
r_mcbond_it2.046
r_mcbond_other2.043
r_angle_refined_deg1.651
r_angle_other_deg0.573
r_chiral_restr0.081
r_gen_planes_refined0.009
r_bond_refined_d0.008
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 Atoms3921
Nucleic Acid Atoms
Solvent Atoms304
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing