7COL

Crystal structure of 5-ketofructose reductase complexed with NADPH


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1NVT 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5295PEG 3350, HEPES-Na, Ammonium fluoride, MPD
Crystal Properties
Matthews coefficientSolvent content
2.0339.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 40.5α = 90
b = 61.528β = 96.82
c = 96.855γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray95CCDADSC QUANTUM 210r2017-05-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NW12A1.0000Photon FactoryAR-NW12A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Rrim I (All)Rpim I (All)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
11.9596.16996.70.060.0720.03913.13.23345133451
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.952.0693.10.1510.1510.1840.1035.13

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1NVT1.9540.2131710172396.440.21130.20850.2637RANDOM24.366
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]
-0.75-1.36-0.171.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.643
r_dihedral_angle_4_deg17.403
r_dihedral_angle_3_deg15.001
r_dihedral_angle_1_deg5.529
r_angle_refined_deg1.428
r_chiral_restr0.088
r_bond_refined_d0.009
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4005
Nucleic Acid Atoms
Solvent Atoms399
Heterogen Atoms96

Software

Software
Software NamePurpose
XDSdata reduction
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MOLREPphasing