8P84 | pdb_00008p84

X-ray structure of Thermoanaerobacterales bacterium monoamine oxidase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelAlphaFold 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.529330% PEG4000, 100 mM tris buffer pH 8.5, 200 mM magnesium chloride
Crystal Properties
Matthews coefficientSolvent content
2.1242

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.931α = 90
b = 94.167β = 90
c = 127.277γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2022-11-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA0.99SLSX06SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.547.131000.0540.0330.99917.66.7131032
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.51.5399.91.1580.7090.6891.76.9

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 REPLACEMENTTHROUGHOUT1.547.13124503643599.960.160280.1590.170.185490.19RANDOM18.618
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]
-0.430.20.23
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.379
r_dihedral_angle_4_deg17.996
r_dihedral_angle_3_deg11.994
r_dihedral_angle_1_deg6.076
r_long_range_B_refined5.066
r_long_range_B_other5.015
r_scangle_other4.328
r_scbond_it2.956
r_scbond_other2.956
r_mcangle_it2.148
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.379
r_dihedral_angle_4_deg17.996
r_dihedral_angle_3_deg11.994
r_dihedral_angle_1_deg6.076
r_long_range_B_refined5.066
r_long_range_B_other5.015
r_scangle_other4.328
r_scbond_it2.956
r_scbond_other2.956
r_mcangle_it2.148
r_mcangle_other2.148
r_angle_other_deg2.031
r_angle_refined_deg1.831
r_mcbond_it1.531
r_mcbond_other1.523
r_chiral_restr0.092
r_bond_refined_d0.014
r_gen_planes_refined0.012
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 Atoms6715
Nucleic Acid Atoms
Solvent Atoms676
Heterogen Atoms115

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing