7P7W

N-acetylglucosamine kinase from Plesiomonas shigelloides compexed with alpha-N-acetylglucosamine and ADP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4DB3 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH291120 mM alcohols; ; 0.1 M imidazole/MES pH 6.5; 30% each glycerol and PEG 4K Condition A3 of Morpheus screen (Molecular dimensions). Crystal was soaked for 60 seconds in cryoprotectant containing 10 mM ADP
Crystal Properties
Matthews coefficientSolvent content
2.550.85

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 115.1α = 90
b = 115.1β = 90
c = 120.304γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 12M2018-05-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.9159DiamondI04-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)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
11.5799.681000.99912.79.9128365
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.571.61000.291

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE4DB31.5799.68128293647199.9810.1870.18570.211229.979
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]
-0.198-0.099-0.1980.644
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.533
r_dihedral_angle_4_deg15.494
r_dihedral_angle_3_deg14.208
r_lrange_it8.07
r_scangle_it6.611
r_dihedral_angle_1_deg5.845
r_scbond_it5.01
r_mcangle_it3.829
r_mcbond_it3.173
r_angle_refined_deg1.447
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.533
r_dihedral_angle_4_deg15.494
r_dihedral_angle_3_deg14.208
r_lrange_it8.07
r_scangle_it6.611
r_dihedral_angle_1_deg5.845
r_scbond_it5.01
r_mcangle_it3.829
r_mcbond_it3.173
r_angle_refined_deg1.447
r_nbtor_refined0.312
r_nbd_refined0.222
r_symmetry_nbd_refined0.201
r_metal_ion_refined0.18
r_symmetry_xyhbond_nbd_refined0.139
r_xyhbond_nbd_refined0.128
r_ncsr_local_group_10.099
r_chiral_restr0.096
r_gen_planes_refined0.008
r_bond_refined_d0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4648
Nucleic Acid Atoms
Solvent Atoms628
Heterogen Atoms207

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MoRDaphasing
xia2data scaling