4DB3 | pdb_00004db3

1.95 Angstrom Resolution Crystal Structure of N-acetyl-D-glucosamine kinase from Vibrio vulnificus.

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2AP1	PDB entry 2AP1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	295	Protein solution: 2.5 mG/mL, 0.3M Sodium chloride, 0.01M HEPES pH 7.5. Screen solution: 0.1M Lithium sulfate, 0.1M Bis-Tris Propane pH 7.0. Cryo: 0.1M Li Sulfate, 0.1M Bis-Tris Propane, 20% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.91	57.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.4	α = 90
b = 80.4	β = 90
c = 110.418	γ = 120

Symmetry
Space Group	P 64

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MARMOSAIC 300 mm CCD	Beryllium lenses	2011-12-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97856	APS	21-ID-G

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.95	30	99.9	0.052	23.1	4.8	29453	29453		-3	32.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.95	1.98	100		0.557	2	4.8	1434

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 2AP1	1.95	29.45	27919	27919	1498	99.94	0.17011	0.17011	0.16848	0.17	0.19848	0.2	RANDOM	36.376

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]
1.53	0.77		1.53		-2.3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.618
r_dihedral_angle_4_deg	11.856
r_dihedral_angle_3_deg	10.158
r_scangle_it	4.623
r_dihedral_angle_1_deg	2.972
r_scbond_it	2.922
r_mcangle_it	1.75
r_angle_refined_deg	1.453
r_mcbond_it	1.029
r_angle_other_deg	0.895

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.618
r_dihedral_angle_4_deg	11.856
r_dihedral_angle_3_deg	10.158
r_scangle_it	4.623
r_dihedral_angle_1_deg	2.972
r_scbond_it	2.922
r_mcangle_it	1.75
r_angle_refined_deg	1.453
r_mcbond_it	1.029
r_angle_other_deg	0.895
r_mcbond_other	0.317
r_chiral_restr	0.096
r_bond_refined_d	0.011
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2358
Nucleic Acid Atoms
Solvent Atoms	193
Heterogen Atoms	14

Software

Software
Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.