Experiment: 6C25

Crystal structure of Adenylosuccinate synthetase from Legionella pneumophila Philadelphia 1 in complex with GDP

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6BS7	native structure, PDB entry 6bs7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	285	Molecular Dimensions Morpheus screen B4: 12.5% w/V PEG 1000, 12.5% w/V PEG 3350, 12.5% V/V MPD: 30mM of each NaF, NaBr, NaI: 100mM MES/imidazole pH 6.5: LepnA.00888.a.B1.PW38319 at 18.4mg/ml + 2mM MgCl2 + 2mM GDP: cryo: direct: tray 297195 b4: puck esb5-10

Crystal Properties
Matthews coefficient	Solvent content
1.92	36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.81	α = 90
b = 90.26	β = 90
c = 60.01	γ = 90

Symmetry
Space Group	P 21 21 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	RIGAKU SATURN 944+		2017-12-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	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	1.9	40.435	99.9	0.066	0.072	0.999	16.09	5.835		30104			25.45

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	1.9	1.95	99		0.534	0.665	0.713	2.08	2.733

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	MOLECULAR REPLACEMENT	THROUGHOUT	native structure, PDB entry 6bs7	1.9	40.435	1.35	30102	2002	99.89	0.1765	0.1739	0.1751	0.2136	0.2137	0	36.6687

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	2962
Nucleic Acid Atoms
Solvent Atoms	218
Heterogen Atoms	30

Software

Software
Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHENIX	phasing
Coot	model building