3PL2

Crystal structure of a 5-keto-2-deoxygluconokinase (NCgl0155, Cgl0158) from Corynebacterium glutamicum ATCC 13032 KITASATO at 1.89 A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2QCV 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.62930.200M NH4OAc, 30.00% PEG-4000, 0.1M Citrate pH 5.6, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.0740.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.908α = 101.86
b = 79.494β = 95.72
c = 81.703γ = 92.11
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2008-10-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-BAPS23-ID-B

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
11.8937.80497.10.0657.82.3872628726225.396
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)
11.891.9495.80.4380.4381.226386

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 REPLACEMENTTHROUGHOUT2QCV1.8937.80487222438496.980.18280.18050.2252RANDOM37.5491
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]
0.230.420.14-0.490.530.54
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.535
r_dihedral_angle_4_deg14.737
r_dihedral_angle_3_deg14.591
r_dihedral_angle_1_deg6.691
r_scangle_it3.121
r_scbond_it1.938
r_angle_refined_deg1.574
r_angle_other_deg1.327
r_mcangle_it1.211
r_mcbond_it0.681
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.535
r_dihedral_angle_4_deg14.737
r_dihedral_angle_3_deg14.591
r_dihedral_angle_1_deg6.691
r_scangle_it3.121
r_scbond_it1.938
r_angle_refined_deg1.574
r_angle_other_deg1.327
r_mcangle_it1.211
r_mcbond_it0.681
r_mcbond_other0.182
r_chiral_restr0.091
r_bond_refined_d0.016
r_gen_planes_refined0.007
r_bond_other_d0.003
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9480
Nucleic Acid Atoms
Solvent Atoms577
Heterogen Atoms13

Software

Software
Software NamePurpose
REFMACrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
MOSFLMdata reduction
MOLREPphasing