2V0I | pdb_00002v0i

Characterization of Substrate Binding and Catalysis of the Potential Antibacterial Target N-acetylglucosamine-1-phosphate Uridyltransferase (GlmU)

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2V0H	PDB ENTRY 2V0H

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6		1.2-1.8M AMMONIUM SULFATE, 2%PEG-400, 0.1M MES PH 5.2-6.1, 20 MM MGCL2, 10 MM UDP-GLCNAC

Crystal Properties
Matthews coefficient	Solvent content
3.65	66.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 107.808	α = 90
b = 107.808	β = 90
c = 233.876	γ = 120

Symmetry
Space Group	P 63 2 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	ADSC CCD		2003-11-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 17-ID		APS	17-ID

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	1.9	50	99.1	0.07	37.9	9		64262

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	1.9	1.97	99.9		0.32	4.5

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	PDB ENTRY 2V0H	1.89	119.52	60974	3260	98.3	0.194	0.193	0.2	0.21	0.22	RANDOM	21.81

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]
1.25	0.62		1.25		-1.87

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.74
r_scangle_it	3.371
r_scbond_it	1.954
r_angle_refined_deg	1.266
r_mcangle_it	1.123
r_angle_other_deg	1.047
r_mcbond_it	0.565
r_symmetry_vdw_other	0.319
r_nbd_other	0.238
r_symmetry_vdw_refined	0.192
r_nbd_refined	0.191
r_symmetry_hbond_refined	0.188
r_xyhbond_nbd_refined	0.121
r_chiral_restr	0.116
r_nbtor_other	0.083
r_bond_refined_d	0.008
r_gen_planes_refined	0.005
r_gen_planes_other	0.004
r_bond_other_d	0.003
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3415
Nucleic Acid Atoms
Solvent Atoms	304
Heterogen Atoms	102

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing