6CN1

2.75 Angstrom Resolution Crystal Structure of UDP-N-acetylglucosamine 1-carboxyvinyltransferase from Pseudomonas putida in Complex with Uridine-diphosphate-2(n-acetylglucosaminyl) butyric acid, (2R)-2-(phosphonooxy)propanoic acid and Magnesium

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5BQ2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	292	Protein: 1.4 mg/ml, 0.5 Sodium chloride, 0.01M Tris pH 8.3, Screen: PACT (B10), 0.2M Magnesium chloride, 0.1M MES buffer pH 6.0, 20% (w/v) PEG 6000

Crystal Properties
Matthews coefficient	Solvent content
2.05	40.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 128.615	α = 90
b = 148.119	β = 90
c = 164.627	γ = 90

Symmetry
Space Group	P 21 21 21

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	MARMOSAIC 300 mm CCD	C(111)	2017-06-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	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	30	99.4	0.136	0.136	0.148	0.058	13	6.4		82344		-3	51.6

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.75	2.8	98.2		0.791	0.791	0.863	0.342	0.714	2.2	6.3

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	5BQ2	2.75	29.95	77560	4127	99.27	0.21167	0.20951	0.25179	RANDOM	51.033

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]
-2.78			-0.17		2.94

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	17.152
r_dihedral_angle_3_deg	7.993
r_dihedral_angle_4_deg	7.209
r_long_range_B_refined	2.571
r_long_range_B_other	2.557
r_dihedral_angle_1_deg	1.657
r_angle_refined_deg	1.202
r_mcangle_it	1.101
r_mcangle_other	1.101
r_scangle_other	1.037
r_angle_other_deg	0.869
r_scbond_it	0.615
r_scbond_other	0.615
r_mcbond_it	0.614
r_mcbond_other	0.614
r_chiral_restr	0.076
r_gen_planes_refined	0.022
r_gen_planes_other	0.02
r_bond_refined_d	0.007
r_bond_other_d	0.001
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	25218
Nucleic Acid Atoms
Solvent Atoms	294
Heterogen Atoms	437

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
MoRDa	phasing