2PNC

Crystal Structure of Bovine Plasma Copper-Containing Amine Oxidase in Complex with Clonidine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1TU5PDB entry 1TU5

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION7.4293KH2PO4 (0.2 M, pH 7.4) and PEG 3350 (20%, w/v), VAPOR DIFFUSION, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.0941.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.36α = 90
b = 131.956β = 90
c = 134.159γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102006-03-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM160.97984ESRFBM16

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
12.43486.80.1293.73477874778744
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)
12.42.5382.10.4071.53.16507

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 1TU52.429.114778745208242986.480.23890.237740.236950.25227RANDOM28.622
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]
0.38-0.31-0.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.803
r_dihedral_angle_4_deg16.823
r_dihedral_angle_3_deg16.722
r_scangle_it6.486
r_mcangle_it5.893
r_scbond_it4.662
r_dihedral_angle_1_deg4.661
r_mcbond_it3.859
r_angle_refined_deg0.877
r_nbtor_refined0.334
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.803
r_dihedral_angle_4_deg16.823
r_dihedral_angle_3_deg16.722
r_scangle_it6.486
r_mcangle_it5.893
r_scbond_it4.662
r_dihedral_angle_1_deg4.661
r_mcbond_it3.859
r_angle_refined_deg0.877
r_nbtor_refined0.334
r_nbd_refined0.23
r_xyhbond_nbd_refined0.204
r_symmetry_hbond_refined0.2
r_symmetry_vdw_refined0.177
r_metal_ion_refined0.13
r_chiral_restr0.063
r_bond_refined_d0.004
r_gen_planes_refined0.002
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_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9852
Nucleic Acid Atoms
Solvent Atoms331
Heterogen Atoms121

Software

Software
Software NamePurpose
REFMACrefinement
ADSCdata collection
MOSFLMdata reduction
SCALAdata scaling
CNSphasing