7PA1

Structure of N-acetylglucosamine kinase from Plesiomonas shigelloides in complex with AMP-PNP in the absence of N-acetylglucoseamine substrate


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH2910.09M NPS; 0.1 M Tris/bicine pH 8.5; 30% each PEG 550 MME and PEG 20K, condition C9 from Morpheus crystallisation screen (Molecular Dimensions).
Crystal Properties
Matthews coefficientSolvent content
2.9658.42

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 121.265α = 90
b = 121.265β = 90
c = 91.684γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2019-07-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.9763DiamondI03

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
12.260.6399.20.9645.23.338637
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)
12.22.270.396

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-VALUE4DB32.239.69338630184699.1680.210.20760.251747.045
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]
0.4170.2090.417-1.353
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.653
r_dihedral_angle_4_deg17.484
r_dihedral_angle_3_deg17.306
r_lrange_it13.405
r_scangle_it12.619
r_scbond_it10.454
r_mcangle_it7.469
r_mcbond_it6.459
r_dihedral_angle_1_deg5.782
r_angle_refined_deg1.563
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.653
r_dihedral_angle_4_deg17.484
r_dihedral_angle_3_deg17.306
r_lrange_it13.405
r_scangle_it12.619
r_scbond_it10.454
r_mcangle_it7.469
r_mcbond_it6.459
r_dihedral_angle_1_deg5.782
r_angle_refined_deg1.563
r_nbtor_refined0.309
r_symmetry_nbd_refined0.225
r_nbd_refined0.205
r_chiral_restr0.119
r_symmetry_xyhbond_nbd_refined0.118
r_xyhbond_nbd_refined0.113
r_ncsr_local_group_10.078
r_bond_refined_d0.007
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4630
Nucleic Acid Atoms
Solvent Atoms152
Heterogen Atoms154

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MoRDaphasing
DMphasing
MOLREPphasing