9H5Q | pdb_00009h5q

Crystal structure of Thermoanaerobacterales bacterium monoamine oxidase in complex with spermidine and its oxidation products


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 8P84 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29330% PEG4000, 100 mM TRIS/HCl buffer pH 8.5, 200 mM MgCl2
Crystal Properties
Matthews coefficientSolvent content
2.0640.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.335α = 90
b = 94.456β = 90
c = 127.74γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293PIXELDECTRIS EIGER R 1M2023-02-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID30B0.9677ESRFID30B

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
11.863.9599.80.99920.319.877126
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.8470.8392.9

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 REPLACEMENTTHROUGHOUT1.863.9573229382399.720.155480.153780.16730.189330.1983RANDOM22.157
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]
0.26-0.11-0.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.8
r_dihedral_angle_4_deg17.601
r_dihedral_angle_3_deg12.371
r_dihedral_angle_1_deg6.264
r_long_range_B_refined5.2
r_long_range_B_other5.147
r_scangle_other4.495
r_scbond_it2.985
r_scbond_other2.985
r_mcangle_other2.361
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.8
r_dihedral_angle_4_deg17.601
r_dihedral_angle_3_deg12.371
r_dihedral_angle_1_deg6.264
r_long_range_B_refined5.2
r_long_range_B_other5.147
r_scangle_other4.495
r_scbond_it2.985
r_scbond_other2.985
r_mcangle_other2.361
r_mcangle_it2.358
r_angle_other_deg1.941
r_mcbond_it1.79
r_mcbond_other1.781
r_angle_refined_deg1.708
r_chiral_restr0.083
r_bond_refined_d0.011
r_gen_planes_refined0.01
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 Atoms6715
Nucleic Acid Atoms
Solvent Atoms518
Heterogen Atoms148

Software

Software
Software NamePurpose
REFMACrefinement