7P7W | pdb_00007p7w

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

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	120 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 coefficient	Solvent content
2.5	50.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 115.1	α = 90
b = 115.1	β = 90
c = 120.304	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 12M		2018-05-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.9159	Diamond	I04-1

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	1.57	99.68	100	0.999	12.7	9.9		128365

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	1.57	1.6	100		0.291

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	4DB3	1.57	99.68	128293	6471	99.981	0.187	0.1857	0.19	0.2112	0.21	29.979

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		-0.198		0.644

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.533
r_dihedral_angle_4_deg	15.494
r_dihedral_angle_3_deg	14.208
r_lrange_it	8.07
r_scangle_it	6.611
r_dihedral_angle_1_deg	5.845
r_scbond_it	5.01
r_mcangle_it	3.829
r_mcbond_it	3.173
r_angle_refined_deg	1.447
r_nbtor_refined	0.312
r_nbd_refined	0.222
r_symmetry_nbd_refined	0.201
r_metal_ion_refined	0.18
r_symmetry_xyhbond_nbd_refined	0.139
r_xyhbond_nbd_refined	0.128
r_ncsr_local_group_1	0.099
r_chiral_restr	0.096
r_gen_planes_refined	0.008
r_bond_refined_d	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4648
Nucleic Acid Atoms
Solvent Atoms	628
Heterogen Atoms	207

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MoRDa	phasing
xia2	data scaling