6WFM | pdb_00006wfm

Crystal structure of UDP-N-acetylglucosamine 1-carboxyvinyltransferase (murA) from Stenotrophomonas maltophilia K279a

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	290	Microlytic MCSG-1 screen, condition g7: 25% (w/V) PEG 3350, 100mM Tris base / HCl pH 8.5: StmaA.00952.a.B1.PW38746 (labelled as StmaA.01067.a.B1.PW38746) at 9mg/ml: tray 314074g7: cryo: 15% EG: puck qvy9-5. For phasing, a crystal from the same condition was incubated for 20sec in a mix of 90% reservoir and 10% 2.5M NaI in EG, followed by a soak for 20sec in a mix of 80% reservoir and 20% NaI in EG. cryo: 20% EG + 500mM NaI: puck ynn3-13

Crystal Properties
Matthews coefficient	Solvent content
2.48	50.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 84.74	α = 90
b = 136.95	β = 90
c = 155.92	γ = 90

Symmetry
Space Group	C 2 2 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	RAYONIX MX-300		2020-02-13	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	RIGAKU SATURN 944+		2020-02-17	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
2	ROTATING ANODE	RIGAKU FR-E+ SUPERBRIGHT	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	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	1.95	37.23	99.8	0.051	0.056	0.999	18.03	6.176		66158			44.8

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.95	2	100		0.595	0.649	0.917	2.61	6.261

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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	SAD	THROUGHOUT	1.95	37.23	1.35	66100	2019	99.77	0.1722	0.1709	0.17	0.2181	0.22	0	49.1715

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	20.959
f_angle_d	0.835
f_chiral_restr	0.055
f_bond_d	0.007
f_plane_restr	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6067
Nucleic Acid Atoms
Solvent Atoms	476
Heterogen Atoms

Software

Software
Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
SHELXDE	phasing
SHELXE	model building
ARP/wARP	model building
Coot	model building

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.