3K7Q

Crystal structure of substrate-bound 6-hydroxy-L-nicotine oxidase from Arthrobacter nicotinovorans


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3K7MPDB ENTRY 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
3.8968.37

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 162.988α = 90
b = 162.988β = 90
c = 162.988γ = 90
Symmetry
Space GroupP 4 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 130 mmKB-mirror2001-11-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID130.782ESRFID13

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.05201000.1090.10922114703947039231.38
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.052.11000.710.713.3113282

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 DIFFRACTIONMOLREPTHROUGHOUTPDB ENTRY 3K7M2.0512.224428344208234399.830.203980.201590.24967RANDOM31.389
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_deg36.28
r_dihedral_angle_4_deg20.192
r_dihedral_angle_3_deg14.73
r_dihedral_angle_1_deg6.8
r_scangle_it6.425
r_scbond_it4.292
r_angle_refined_deg3.007
r_mcangle_it2.75
r_mcbond_it1.808
r_nbtor_refined0.351
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.28
r_dihedral_angle_4_deg20.192
r_dihedral_angle_3_deg14.73
r_dihedral_angle_1_deg6.8
r_scangle_it6.425
r_scbond_it4.292
r_angle_refined_deg3.007
r_mcangle_it2.75
r_mcbond_it1.808
r_nbtor_refined0.351
r_symmetry_vdw_refined0.289
r_nbd_refined0.279
r_symmetry_hbond_refined0.261
r_xyhbond_nbd_refined0.212
r_chiral_restr0.201
r_bond_refined_d0.032
r_gen_planes_refined0.015
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3323
Nucleic Acid Atoms
Solvent Atoms372
Heterogen Atoms109

Software

Software
Software NamePurpose
MAR345data collection
MOLREPphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling