3UXJ

Crystal Structure of 7-cyano-7-deazaguanine reductase, QueF from Vibrio cholerae complexed with NADP and PreQ0


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3S19PDB entry 3S19

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.22890.2 M sodium chloride, 0.1 M sodium potassium phosphate pH 6.2, 20 % (w/v) PEG-1000, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.0439.73

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.387α = 110.01
b = 71.416β = 119.54
c = 71.358γ = 99.46
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210rmirrors2010-12-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-BM0.97903APS19-BM

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
11.45094.10.02617.62.419472319472310.85
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.41.4267.10.13952.16903

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 3S191.40127.009194705194705981094.090.1340.1340.1320.165random14.2
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]
0.5345-0.7416-0.3987-1.284-1.93090.7494
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d17.144
f_angle_d1.844
f_chiral_restr0.135
f_bond_d0.018
f_plane_restr0.01
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8342
Nucleic Acid Atoms
Solvent Atoms1112
Heterogen Atoms166

Software

Software
Software NamePurpose
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
MOLREPphasing
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling