3RZP

Crystal Structure of the C194A mutant of 7-cyano-7-deazaguanine reductase, QueF from Vibrio cholerae complexed with preQ1


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3BP1PDB ENTRY 3BP1

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52890.2 M Sodium acetate, 0.1 M Tris pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.0439.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.316α = 110.43
b = 71.192β = 119.22
c = 71.463γ = 99.33
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rmirrors2010-11-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.97937APS19-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
125095.80.0788.71.8689726897232.69
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)
122.0393.20.371.91.63394

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 3BP1235.0246790767907344695.660.1740.1740.1710.221random43
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]
-4.4282-6.88093.7935-5.75930.393110.1875
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d15.726
f_angle_d1.217
f_chiral_restr0.098
f_bond_d0.007
f_plane_restr0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8230
Nucleic Acid Atoms
Solvent Atoms470
Heterogen Atoms64

Software

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