7P7I | pdb_00007p7i

Native structure of N-acetylglucosamine kinase from Plesiomonas shigelloides

X-RAY DIFFRACTION

---

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 Tris/bicine pH 8.5; 12.5% each MPD, PEG 1K, PEG 3350. condition A12 from Morpheus screen (Molecular Dimensions)

Crystal Properties
Matthews coefficient	Solvent content
2.57	52.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 95.23	α = 90
b = 95.23	β = 90
c = 180.55	γ = 120

Symmetry
Space Group	P 31 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 PILATUS3 6M		2017-09-27	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	1.7	75.01	99.6	0.999	13.8	5		104319

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	1.7	1.73	99.7		0.27		5.1

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	1.7	60.888	104239	5218	99.517	0.184	0.1827	0.18	0.2103	0.21	43.654

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]
1.128	0.564		1.128		-3.66

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.223
r_dihedral_angle_4_deg	17.493
r_dihedral_angle_3_deg	15.679
r_lrange_it	9.044
r_scangle_it	8.742
r_scbond_it	7.307
r_dihedral_angle_1_deg	5.663
r_mcangle_it	5.284
r_mcbond_it	4.784
r_angle_refined_deg	1.617
r_nbtor_refined	0.314
r_nbd_refined	0.205
r_symmetry_nbd_refined	0.205
r_symmetry_xyhbond_nbd_refined	0.138
r_xyhbond_nbd_refined	0.122
r_chiral_restr	0.114
r_ncsr_local_group_1	0.094
r_bond_refined_d	0.009
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4639
Nucleic Acid Atoms
Solvent Atoms	513
Heterogen Atoms	84

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MoRDa	phasing
DM	model building
BUSTER	refinement