7P9P

N-acetylglucosamine kinase from Plesiomonas shigelloides compexed with alpha-N-acetylglucosamine and AMP-PNP inhibitor

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	60 mM divalent cations; 0.1 M imidazole/MES pH 6.5; 30% each glycerol and PEG 4K. Condition A3 from Morpheus screen (Molecular Dimensions)

Crystal Properties
Matthews coefficient	Solvent content
2.51	50.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 115.202	α = 90
b = 115.202	β = 90
c = 120.36	γ = 120

Symmetry
Space Group	P 32 2 1

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		2018-10-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	Diamond	I04

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	2.11	57.6	100	0.998	9.5	10		53533

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	2.11	2.17			0.336

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	2.11	29.107	53472	2794	99.935	0.194	0.1914	0.233	50.004

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]
-1.845	-0.923		-1.845		5.986

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.611
r_dihedral_angle_4_deg	18.71
r_dihedral_angle_3_deg	16.602
r_lrange_it	12.784
r_scangle_it	11.505
r_scbond_it	9.263
r_mcangle_it	8.212
r_mcbond_it	6.802
r_dihedral_angle_1_deg	5.817
r_angle_refined_deg	1.565
r_nbtor_refined	0.314
r_nbd_refined	0.217
r_symmetry_nbd_refined	0.174
r_symmetry_xyhbond_nbd_refined	0.139
r_xyhbond_nbd_refined	0.118
r_metal_ion_refined	0.113
r_chiral_restr	0.106
r_ncsr_local_group_1	0.089
r_bond_refined_d	0.007
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4650
Nucleic Acid Atoms
Solvent Atoms	257
Heterogen Atoms	199

Software

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