2H0U

Crystal structure of NAD(P)H-flavin oxidoreductase from Helicobacter pylori


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.62890.1M Na(OAC), 27% PEG2KMME, 5mM FMN, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.1643.05

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.035α = 90
b = 87.178β = 90
c = 94.979γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152005-12-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.9794APS19-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.8950990.0874551845318268-3
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)
11.891.9692.90.18212.84.61685

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUT1.947.51170631706391999.660.179880.179880.177710.22054RANDOM18.295
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]
0.360.52-0.88
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.203
r_dihedral_angle_3_deg13.665
r_dihedral_angle_4_deg10.819
r_dihedral_angle_1_deg5.707
r_scangle_it4.338
r_scbond_it3.026
r_mcangle_it1.541
r_mcbond_it1.468
r_angle_refined_deg1.422
r_nbtor_refined0.307
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.203
r_dihedral_angle_3_deg13.665
r_dihedral_angle_4_deg10.819
r_dihedral_angle_1_deg5.707
r_scangle_it4.338
r_scbond_it3.026
r_mcangle_it1.541
r_mcbond_it1.468
r_angle_refined_deg1.422
r_nbtor_refined0.307
r_symmetry_hbond_refined0.254
r_nbd_refined0.214
r_symmetry_vdw_refined0.187
r_xyhbond_nbd_refined0.183
r_chiral_restr0.098
r_bond_refined_d0.017
r_gen_planes_refined0.008
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 Atoms1595
Nucleic Acid Atoms
Solvent Atoms216
Heterogen Atoms31

Software

Software
Software NamePurpose
REFMACrefinement
SBC-Collectdata collection
HKL-2000data scaling
HKL-3000phasing
SHELXEmodel building
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building