6RKP

Crystal structure of human monoamine oxidase B in complex with styrylpiperidine analogue 84


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5277PEG 4000, lithium sulphate, ADA buffer
Crystal Properties
Matthews coefficientSolvent content
2.7455.08

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 132.908α = 90
b = 223.657β = 90
c = 86.721γ = 90
Symmetry
Space GroupC 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2017-11-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID30B0.98ESRFID30B

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.747.7199.90.0960.99811.76.8141411
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.71.731.6660.503

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 REPLACEMENTTHROUGHOUT2v5z1.747.7137863354599.920.181990.181370.20558RANDOM23.534
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]
1.65-0.63-1.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.147
r_dihedral_angle_4_deg16.234
r_dihedral_angle_3_deg13.916
r_dihedral_angle_1_deg6.281
r_long_range_B_refined4.68
r_long_range_B_other4.59
r_scangle_other3.426
r_scbond_it2.139
r_scbond_other2.139
r_mcangle_it1.993
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.147
r_dihedral_angle_4_deg16.234
r_dihedral_angle_3_deg13.916
r_dihedral_angle_1_deg6.281
r_long_range_B_refined4.68
r_long_range_B_other4.59
r_scangle_other3.426
r_scbond_it2.139
r_scbond_other2.139
r_mcangle_it1.993
r_mcangle_other1.993
r_angle_other_deg1.478
r_angle_refined_deg1.365
r_mcbond_it1.328
r_mcbond_other1.328
r_chiral_restr0.065
r_bond_refined_d0.008
r_gen_planes_refined0.006
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 Atoms7914
Nucleic Acid Atoms
Solvent Atoms769
Heterogen Atoms186

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing