3NG7

Complex of dithionite-reduced 6-hydroxy-L-nicotine oxidase with substrate bound at active site and inhibitor at exit cavity


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.529820mM Sodium phosphate, 4M sodium formiate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
3.8868.27

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 163.771α = 90
b = 163.771β = 90
c = 163.771γ = 90
Symmetry
Space GroupP 4 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mmmirror2003-03-21MSINGLE 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
11.952099.60.11555516454943225.95
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)
11.951.97960.70224.52733

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 3K7M1.9514.45494351749276699.580.169010.167150.20385RANDOM27.643
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_deg37.188
r_dihedral_angle_4_deg18.4
r_dihedral_angle_3_deg15.573
r_dihedral_angle_1_deg7.072
r_scangle_it6.434
r_scbond_it4.382
r_mcangle_it2.606
r_angle_refined_deg2.542
r_mcbond_it1.764
r_nbtor_refined0.326
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.188
r_dihedral_angle_4_deg18.4
r_dihedral_angle_3_deg15.573
r_dihedral_angle_1_deg7.072
r_scangle_it6.434
r_scbond_it4.382
r_mcangle_it2.606
r_angle_refined_deg2.542
r_mcbond_it1.764
r_nbtor_refined0.326
r_symmetry_vdw_refined0.239
r_symmetry_hbond_refined0.236
r_nbd_refined0.23
r_chiral_restr0.226
r_xyhbond_nbd_refined0.224
r_bond_refined_d0.033
r_gen_planes_refined0.015
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3292
Nucleic Acid Atoms
Solvent Atoms516
Heterogen Atoms122

Software

Software
Software NamePurpose
MAR345data collection
MOLREPphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling