Experiment: 6WCT

Crystal structure of a guanylate kinase from Stenotrophomonas maltophilia K279a bound to guanosine-5'-monophosphate

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3TR0	PDB entry 3TR0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	287	33 mg/mL StmaA.01463.a.B1.PW38755 in 7 mM magnesium chloride, 7 mM ATP, 7 mM GMP (5GP) against MCSG1 screen condition B1 (0.6 M sodium chloride, 0.1 M MES, pH 6.5, 20% PEG4000), supplemented with 20% ethylene glycol as cryoprotectant, unique puck ID pfi1-7, crystal tracking ID 314557b1

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.66	α = 90
b = 101.42	β = 92.03
c = 70.02	γ = 90

Symmetry
Space Group	P 1 21 1

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 MX300-HS		2020-03-19	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)	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	2.1	47.51	99.9	0.044	0.05	0.999	18.97	4.665		51005			48.413

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	2.1	2.15	100		0.578	0.652	0.903	2.98	4.688

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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 3TR0	2.1	47.51	47846	2890	93.71	0.1822	0.1792	0.1813	0.2294	0.2316	57.0784

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]

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6125
Nucleic Acid Atoms
Solvent Atoms	286
Heterogen Atoms	105

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction