3SPT | pdb_00003spt

Crystal structure of GlmU from Mycobacterium tuberculosis in complex with ACETYL COENZYME A and URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3DJ4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	sitting drop	8.5	291	0.1M Tris-Cl, pH-8.5, 2% Tacsimate, 18% PEG 3350, sitting drop, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
4.02	69.43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 110.194	α = 90
b = 110.194	β = 90
c = 361.295	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	100	CCD	MARCCD 225	mirrors	2011-01-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM14	0.97625	ESRF	BM14

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	2.33	19.808	99.8	0.054	24.88			36542		-3	42.057

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.33	2.39	98.3		0.359	0.387	5.05

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3DJ4	2.33	19.68	35443	1001	99.85	0.19291	0.19205	0.19	0.22359	0.23	RANDOM	31.524

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]
					0.0001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.4
r_dihedral_angle_4_deg	22.17
r_dihedral_angle_3_deg	17.29
r_dihedral_angle_1_deg	7.186
r_scangle_it	6.09
r_scbond_it	3.798
r_angle_refined_deg	2.353
r_mcangle_it	2.173
r_mcbond_it	1.189
r_chiral_restr	0.246
r_bond_refined_d	0.026
r_gen_planes_refined	0.011
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3471
Nucleic Acid Atoms
Solvent Atoms	212
Heterogen Atoms	93

Software

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