7P9L

N-acetylglucosamine kinase from Plesiomonas shigelloides compexed with alpha-N-acetylglucosamine-6-phosphate

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	90 mM halogens; 0.1 M Tris/bicine pH 8.5; 30% each PEG 550 MME and PEG 20K, condition B9 from Morpheus screen (Molecular Dimensions)

Crystal Properties
Matthews coefficient	Solvent content
3.42	64.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 114.508	α = 90
b = 114.508	β = 90
c = 119.266	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		2016-11-28	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	1.75	99.17	99.1	0.998	8.4	3.8		90389

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	1.75	1.78			0.194

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	1.75	76.252	90350	4568	99.02	0.194	0.1929	0.2226	36.515

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]
-0.012	-0.006		-0.012		0.038

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.837
r_dihedral_angle_4_deg	15.786
r_dihedral_angle_3_deg	15.214
r_lrange_it	11.616
r_scangle_it	10.111
r_scbond_it	8.059
r_mcangle_it	7.299
r_mcbond_it	6.253
r_dihedral_angle_1_deg	5.724
r_angle_refined_deg	1.75
r_metal_ion_refined	0.345
r_nbtor_refined	0.318
r_symmetry_nbd_refined	0.23
r_nbd_refined	0.214
r_xyhbond_nbd_refined	0.139
r_chiral_restr	0.112
r_symmetry_xyhbond_nbd_refined	0.111
r_ncsr_local_group_1	0.093
r_bond_refined_d	0.012
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4646
Nucleic Acid Atoms
Solvent Atoms	353
Heterogen Atoms	200

Software

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