2BYB | pdb_00002byb

Human Monoamine Oxidase B in complex with Deprenyl


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1S2QPDB ENTRY 1S2Q

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.2pH 6.20
Crystal Properties
Matthews coefficientSolvent content
2.7347

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 132.835α = 90
b = 225.84β = 90
c = 85.68γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2004-10-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-2ESRFID14-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.21595.90.09112.760540
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.398.40.4133.1

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1S2Q2.215605401605950.2390.2370.40.2990.42RANDOM32.6
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]
-2.345.17-2.83
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.131
r_dihedral_angle_4_deg19.561
r_dihedral_angle_3_deg16.666
r_dihedral_angle_1_deg6.732
r_scangle_it2.95
r_scbond_it2.173
r_angle_refined_deg1.715
r_mcangle_it1.205
r_mcbond_it0.796
r_symmetry_hbond_refined0.542
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.131
r_dihedral_angle_4_deg19.561
r_dihedral_angle_3_deg16.666
r_dihedral_angle_1_deg6.732
r_scangle_it2.95
r_scbond_it2.173
r_angle_refined_deg1.715
r_mcangle_it1.205
r_mcbond_it0.796
r_symmetry_hbond_refined0.542
r_nbtor_refined0.306
r_symmetry_vdw_refined0.271
r_nbd_refined0.215
r_xyhbond_nbd_refined0.196
r_chiral_restr0.109
r_bond_refined_d0.017
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7911
Nucleic Acid Atoms
Solvent Atoms489
Heterogen Atoms134

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
CCP4phasing