3NH3

Complex of 6-hydroxy-L-nicotine oxidase with final ketone product formed during catalytic turnover


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3K7MPDB code 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
3.8367.85

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 163.051α = 90
b = 163.051β = 90
c = 163.051γ = 90
Symmetry
Space GroupP 4 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mmmirror2003-03-17MSINGLE 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
12.1201000.116208.54367943679231.4
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)
12.12.141000.7042.58.52137

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 code 3K7M2.112.224127441266218499.980.160770.158550.20372RANDOM31.533
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_deg40.207
r_dihedral_angle_4_deg19.739
r_dihedral_angle_3_deg16.248
r_scangle_it6.741
r_dihedral_angle_1_deg6.63
r_scbond_it4.484
r_mcangle_it2.74
r_angle_refined_deg2.369
r_mcbond_it1.846
r_symmetry_hbond_refined0.519
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.207
r_dihedral_angle_4_deg19.739
r_dihedral_angle_3_deg16.248
r_scangle_it6.741
r_dihedral_angle_1_deg6.63
r_scbond_it4.484
r_mcangle_it2.74
r_angle_refined_deg2.369
r_mcbond_it1.846
r_symmetry_hbond_refined0.519
r_symmetry_vdw_refined0.392
r_nbtor_refined0.327
r_nbd_refined0.242
r_xyhbond_nbd_refined0.218
r_chiral_restr0.208
r_bond_refined_d0.031
r_gen_planes_refined0.014
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 Atoms3270
Nucleic Acid Atoms
Solvent Atoms393
Heterogen Atoms123

Software

Software
Software NamePurpose
MAR345data collection
MOLREPphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling