7PA1

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

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4DB3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH		291	0.09M 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 coefficient	Solvent content
2.96	58.42

Crystal Data

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

Symmetry
Space Group	P 65

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M		2019-07-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9763	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.2	60.63	99.2	0.964	5.2	3.3		38637

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.27			0.396

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	4DB3	2.2	39.693	38630	1846	99.168	0.21	0.2076	0.2517	47.045

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]
0.417	0.209		0.417		-1.353

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.653
r_dihedral_angle_4_deg	17.484
r_dihedral_angle_3_deg	17.306
r_lrange_it	13.405
r_scangle_it	12.619
r_scbond_it	10.454
r_mcangle_it	7.469
r_mcbond_it	6.459
r_dihedral_angle_1_deg	5.782
r_angle_refined_deg	1.563
r_nbtor_refined	0.309
r_symmetry_nbd_refined	0.225
r_nbd_refined	0.205
r_chiral_restr	0.119
r_symmetry_xyhbond_nbd_refined	0.118
r_xyhbond_nbd_refined	0.113
r_ncsr_local_group_1	0.078
r_bond_refined_d	0.007
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4630
Nucleic Acid Atoms
Solvent Atoms	152
Heterogen Atoms	154

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MoRDa	phasing
DM	phasing
MOLREP	phasing