3K7T

Crystal structure of apo-form 6-hydroxy-L-nicotine oxidase, crystal form P3121


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52890.1M Hepes, 1.5M lithium sulfate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
4.773.84

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 122.957α = 90
b = 122.957β = 90
c = 199.918γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mmmirrors2002-12-12MSINGLE 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)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
12.852099.20.0780.07825.37.54141541084272.9
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)
2.852.91000.750.7527.52038

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 3K7M2.8516.63919738462203598.140.277760.275490.32118RANDOM72.942
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]
3.721.863.72-5.58
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.675
r_dihedral_angle_3_deg18.815
r_dihedral_angle_4_deg17.515
r_dihedral_angle_1_deg7.599
r_scangle_it4.256
r_scbond_it2.467
r_mcangle_it1.853
r_angle_refined_deg1.781
r_mcbond_it1.021
r_nbtor_refined0.322
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.675
r_dihedral_angle_3_deg18.815
r_dihedral_angle_4_deg17.515
r_dihedral_angle_1_deg7.599
r_scangle_it4.256
r_scbond_it2.467
r_mcangle_it1.853
r_angle_refined_deg1.781
r_mcbond_it1.021
r_nbtor_refined0.322
r_symmetry_vdw_refined0.294
r_nbd_refined0.233
r_xyhbond_nbd_refined0.167
r_symmetry_hbond_refined0.161
r_chiral_restr0.103
r_bond_refined_d0.018
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6540
Nucleic Acid Atoms
Solvent Atoms42
Heterogen Atoms192

Software

Software
Software NamePurpose
MAR345data collection
MOLREPphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling