9H5Z | pdb_00009h5z

Crystal structure of Thermoanaerobacterales bacterium monoamine oxidase in complex with benzylamine


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
2.141.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 69.473α = 90
b = 100.242β = 90
c = 120.901γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293PIXELDECTRIS EIGER R 1M2023-05-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-20.873128ESRFID23-2

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
11.1477.171000.9969.41343665
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)
12.22.2570.8132.5

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 REPLACEMENTTHROUGHOUT2.277.1741489205199.840.181510.178710.18950.239560.248RANDOM38.629
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]
-2.934.56-1.63
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.755
r_dihedral_angle_4_deg16.838
r_dihedral_angle_3_deg14.479
r_dihedral_angle_1_deg6.728
r_long_range_B_other6.673
r_long_range_B_refined6.672
r_scangle_other5.333
r_mcangle_it4.153
r_mcangle_other4.151
r_scbond_it3.545
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.755
r_dihedral_angle_4_deg16.838
r_dihedral_angle_3_deg14.479
r_dihedral_angle_1_deg6.728
r_long_range_B_other6.673
r_long_range_B_refined6.672
r_scangle_other5.333
r_mcangle_it4.153
r_mcangle_other4.151
r_scbond_it3.545
r_scbond_other3.545
r_mcbond_it2.952
r_mcbond_other2.949
r_angle_other_deg1.802
r_angle_refined_deg1.637
r_chiral_restr0.068
r_bond_refined_d0.009
r_gen_planes_refined0.007
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 Atoms6700
Nucleic Acid Atoms
Solvent Atoms237
Heterogen Atoms116

Software

Software
Software NamePurpose
REFMACrefinement