3CXQ

Crystal structure of human glucosamine 6-phosphate N-acetyltransferase 1 bound to GlcN6P

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2HUZ	PDB ENTRY 2HUZ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	289	0.2M Na formate, 25% w/v PEG 3350, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.44	49.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.136	α = 90
b = 54.136	β = 90
c = 138.638	γ = 90

Symmetry
Space Group	P 43 21 2

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	BRUKER SMART 6000	Montel mirrors	2008-03-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	BRUKER AXS MICROSTAR	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	2.3	54.348	90.38	0.063	9.2	6.04		8884

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.3	2.46			0.322	1.3

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2HUZ	2.3	20	8861	424	90.21	0.209	0.207	0.255	RANDOM	25.641

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]
1.6			1.6		-3.2

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.35
r_dihedral_angle_3_deg	15.451
r_dihedral_angle_4_deg	12.718
r_dihedral_angle_1_deg	5.57
r_scangle_it	1.595
r_angle_refined_deg	1.139
r_scbond_it	0.959
r_mcangle_it	0.752
r_mcbond_it	0.437
r_nbtor_refined	0.294

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.35
r_dihedral_angle_3_deg	15.451
r_dihedral_angle_4_deg	12.718
r_dihedral_angle_1_deg	5.57
r_scangle_it	1.595
r_angle_refined_deg	1.139
r_scbond_it	0.959
r_mcangle_it	0.752
r_mcbond_it	0.437
r_nbtor_refined	0.294
r_symmetry_hbond_refined	0.239
r_nbd_refined	0.185
r_symmetry_vdw_refined	0.182
r_xyhbond_nbd_refined	0.14
r_chiral_restr	0.07
r_bond_refined_d	0.009
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1430
Nucleic Acid Atoms
Solvent Atoms	89
Heterogen Atoms	16

Software

Software
Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
LSCALE	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.