4DB3

1.95 Angstrom Resolution Crystal Structure of N-acetyl-D-glucosamine kinase from Vibrio vulnificus.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2AP1PDB entry 2AP1

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7295Protein solution: 2.5 mG/mL, 0.3M Sodium chloride, 0.01M HEPES pH 7.5. Screen solution: 0.1M Lithium sulfate, 0.1M Bis-Tris Propane pH 7.0. Cryo: 0.1M Li Sulfate, 0.1M Bis-Tris Propane, 20% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.9157.79

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.4α = 90
b = 80.4β = 90
c = 110.418γ = 120
Symmetry
Space GroupP 64

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDBeryllium lenses2011-12-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.97856APS21-ID-G

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.953099.90.05223.14.82945329453-332.7
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)
11.951.981000.55724.81434

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 2AP11.9529.452791927919149899.940.170110.170110.168480.19848RANDOM36.376
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]
1.530.771.53-2.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.618
r_dihedral_angle_4_deg11.856
r_dihedral_angle_3_deg10.158
r_scangle_it4.623
r_dihedral_angle_1_deg2.972
r_scbond_it2.922
r_mcangle_it1.75
r_angle_refined_deg1.453
r_mcbond_it1.029
r_angle_other_deg0.895
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.618
r_dihedral_angle_4_deg11.856
r_dihedral_angle_3_deg10.158
r_scangle_it4.623
r_dihedral_angle_1_deg2.972
r_scbond_it2.922
r_mcangle_it1.75
r_angle_refined_deg1.453
r_mcbond_it1.029
r_angle_other_deg0.895
r_mcbond_other0.317
r_chiral_restr0.096
r_bond_refined_d0.011
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2358
Nucleic Acid Atoms
Solvent Atoms193
Heterogen Atoms14

Software

Software
Software NamePurpose
Blu-Icedata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling