2QKX

N-acetyl glucosamine 1-phosphate uridyltransferase from Mycobacterium tuberculosis complex with N-acetyl glucosamine 1-phosphate

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1HM9	PDB entry 1HM9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	291	0.2M Lithium nitrate, 20% PEG 3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
3.02	59.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 94.303	α = 90
b = 94.303	β = 90
c = 288.041	γ = 120

Symmetry
Space Group	H 3 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	110	IMAGE PLATE	MAR scanner 345 mm plate	osmic	2007-06-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007	1.5418

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	2.75	42.33	100	0.151	13.2	6.3	13239	13239

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	2.75	2.9	100		0.623	3	6.3	1892

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1HM9	2.75	40.42	12588	12588	651	99.95	0.19791	0.19791	0.19514	0.25071	RANDOM	27.107

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]
-0.65	-0.32		-0.65		0.97

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.028
r_dihedral_angle_4_deg	19.322
r_dihedral_angle_3_deg	16.716
r_dihedral_angle_1_deg	7.136
r_scangle_it	2.599
r_angle_refined_deg	1.673
r_scbond_it	1.611
r_mcangle_it	1.14
r_mcbond_it	0.631
r_nbtor_refined	0.315

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.028
r_dihedral_angle_4_deg	19.322
r_dihedral_angle_3_deg	16.716
r_dihedral_angle_1_deg	7.136
r_scangle_it	2.599
r_angle_refined_deg	1.673
r_scbond_it	1.611
r_mcangle_it	1.14
r_mcbond_it	0.631
r_nbtor_refined	0.315
r_nbd_refined	0.238
r_symmetry_hbond_refined	0.211
r_symmetry_vdw_refined	0.184
r_xyhbond_nbd_refined	0.14
r_chiral_restr	0.092
r_bond_refined_d	0.016
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2795
Nucleic Acid Atoms
Solvent Atoms	39
Heterogen Atoms	19

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345dtb	data collection
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

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.