6FVZ

Crystal structure of human monoamine oxidase B (MAO B) in complex with dimethylphenyl-chromone-carboxamide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2V5Z 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP27712% PEG4000, 100 mM ADA buffer pH 6.5, 70 mM lithium sulphate
Crystal Properties
Matthews coefficientSolvent content
2.6854.18

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 131.182α = 90
b = 222.753β = 90
c = 86.482γ = 90
Symmetry
Space GroupC 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 X 2M2016-09-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-20.987ESRFID23-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)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
11.84799.40.1640.10210.26.8117061
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.83

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2v5z1.847114120294099.970.168950.168170.1987RANDOM17.89
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]
1.25-1.16-0.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.37
r_dihedral_angle_4_deg14.731
r_dihedral_angle_3_deg13.262
r_dihedral_angle_1_deg6.086
r_long_range_B_refined4.084
r_long_range_B_other3.917
r_scangle_other2.608
r_mcangle_it1.623
r_mcangle_other1.623
r_scbond_it1.611
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.37
r_dihedral_angle_4_deg14.731
r_dihedral_angle_3_deg13.262
r_dihedral_angle_1_deg6.086
r_long_range_B_refined4.084
r_long_range_B_other3.917
r_scangle_other2.608
r_mcangle_it1.623
r_mcangle_other1.623
r_scbond_it1.611
r_scbond_other1.61
r_angle_other_deg1.522
r_angle_refined_deg1.481
r_mcbond_it1.006
r_mcbond_other1.005
r_chiral_restr0.086
r_bond_refined_d0.011
r_gen_planes_refined0.007
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 Atoms7926
Nucleic Acid Atoms
Solvent Atoms842
Heterogen Atoms188

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing