3NHO

Complex of 6-hydroxy-L-nicotine oxidase with product bound at active site


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.529320mM Sodium phosphate; 4M sodium formiate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.9468.82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 164.723α = 90
b = 164.723β = 90
c = 164.723γ = 90
Symmetry
Space GroupP 4 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mmMIRROR2004-06-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMPG/DESY, HAMBURG BEAMLINE BW6MPG/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
12.852099.80.145151518369247
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)
12.852.921000.7452.515

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 3K7M2.8514.4173221729894499.90.1690.1650.243RANDOM46.71
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_deg36.192
r_dihedral_angle_4_deg19.971
r_dihedral_angle_3_deg19.132
r_dihedral_angle_1_deg7.075
r_scangle_it4.396
r_scbond_it2.532
r_angle_refined_deg1.89
r_mcangle_it1.833
r_mcbond_it1.009
r_nbtor_refined0.328
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.192
r_dihedral_angle_4_deg19.971
r_dihedral_angle_3_deg19.132
r_dihedral_angle_1_deg7.075
r_scangle_it4.396
r_scbond_it2.532
r_angle_refined_deg1.89
r_mcangle_it1.833
r_mcbond_it1.009
r_nbtor_refined0.328
r_nbd_refined0.241
r_xyhbond_nbd_refined0.197
r_symmetry_vdw_refined0.192
r_symmetry_hbond_refined0.186
r_chiral_restr0.105
r_bond_refined_d0.019
r_gen_planes_refined0.006
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 Atoms458
Heterogen Atoms110

Software

Software
Software NamePurpose
MAR345data collection
MOLREPphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling