3DJ4 | pdb_00003dj4

Crystal Structure of GlmU from Mycobacterium tuberculosis in complex with URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE.

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	277	8% PEG 8000, 150mM NaCl, 2mM MnCl2, 5% Glycerol, 1,3-butanediol, AMPPNP, MgCl2, DTT, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.2	61.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.6	α = 90
b = 78.6	β = 90
c = 278	γ = 120

Symmetry
Space Group	H 3

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	MAR scanner 345 mm plate	mirrors		M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.54179

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	2.38		98.3	0.097	19.84			25334		-3	31.363

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)
	2.38	2.44	82.3		0.443	4.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	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		THROUGHOUT	2.38	29.03	25333	1267	100	0.197	0.194	0.2	0.257	0.26	RANDOM	24.694

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]
0.86	0.43		0.86		-1.29

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.116
r_dihedral_angle_4_deg	22.214
r_dihedral_angle_3_deg	15.849
r_dihedral_angle_1_deg	8.467
r_scangle_it	5.457
r_scbond_it	3.574
r_angle_refined_deg	2.544
r_mcangle_it	2.125
r_mcbond_it	1.286
r_nbtor_refined	0.302

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.116
r_dihedral_angle_4_deg	22.214
r_dihedral_angle_3_deg	15.849
r_dihedral_angle_1_deg	8.467
r_scangle_it	5.457
r_scbond_it	3.574
r_angle_refined_deg	2.544
r_mcangle_it	2.125
r_mcbond_it	1.286
r_nbtor_refined	0.302
r_nbd_refined	0.247
r_symmetry_vdw_refined	0.243
r_xyhbond_nbd_refined	0.192
r_symmetry_hbond_refined	0.147
r_chiral_restr	0.137
r_bond_refined_d	0.027
r_gen_planes_refined	0.008
r_metal_ion_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3374
Nucleic Acid Atoms
Solvent Atoms	147
Heterogen Atoms	41

Software

Software
Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection

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.