3NN6

Crystal structure of inhibitor-bound in active centre 6-hydroxy-L-nicotine oxidase from Arthrobacter nicotinovorans


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3K7MPDB 3K7M

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.529320mM Sodium phosphate; 4M sodium formiate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.9168.51

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 164.184α = 90
b = 164.184β = 90
c = 164.184γ = 90
Symmetry
Space GroupP 4 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mmmirror2009-09-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMPG/DESY, HAMBURG BEAMLINE BW61.05MPG/DESY, HAMBURGBW6

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
12.192099.80.08521.55.53939139330234.8
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)
12.192.231000.64535.51909

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB 3K7M2.1914.43811037196196299.70.170460.168270.21249RANDOM30.743
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.127
r_dihedral_angle_4_deg20.117
r_dihedral_angle_3_deg15.436
r_dihedral_angle_1_deg6.732
r_scangle_it5.777
r_scbond_it4.007
r_angle_refined_deg2.34
r_mcangle_it2.333
r_mcbond_it1.562
r_symmetry_vdw_refined0.438
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.127
r_dihedral_angle_4_deg20.117
r_dihedral_angle_3_deg15.436
r_dihedral_angle_1_deg6.732
r_scangle_it5.777
r_scbond_it4.007
r_angle_refined_deg2.34
r_mcangle_it2.333
r_mcbond_it1.562
r_symmetry_vdw_refined0.438
r_symmetry_hbond_refined0.364
r_nbtor_refined0.32
r_nbd_refined0.241
r_xyhbond_nbd_refined0.191
r_chiral_restr0.19
r_bond_refined_d0.03
r_gen_planes_refined0.011
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3272
Nucleic Acid Atoms
Solvent Atoms430
Heterogen Atoms109

Software

Software
Software NamePurpose
MAR345data collection
MOLREPphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling