5VK4

Crystal structure of a phosphoribosylformylglycinamidine cyclo-ligase from Neisseria gonorrhoeae bound to AMPPNP and magnesium

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1CLI

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	289	NegoA.00263.a.B1.PW37900 at 18.3 mg/mL with 3 mM MgCl2 and 3 mM AMPPNP against MCSG1 screen condition B4 which contains 0.2 M MgCl2, 0.1 M BisTris pH 6.5, and 25% PEG 3350, supplemented with 15% EG as cryo protectant,crystal tracking ID 273610b4

Crystal Properties
Matthews coefficient	Solvent content
2.13	42.33

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.25	α = 90
b = 79.61	β = 90
c = 150.07	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		2017-03-12	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	2.65	44.831	99.2	0.082	0.092	0.997	15.35	5.003		19414		-3	47.64

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	2.65	2.72	99.9		0.629	0.704	0.806	2.67	5.11

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	NONE	1CLI	2.65	44.831	1.36	19411	978	99.2	0.1876	0.1846	0.2443	53.0209

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	14.658
f_angle_d	0.758
f_chiral_restr	0.05
f_plane_restr	0.006
f_bond_d	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4727
Nucleic Acid Atoms
Solvent Atoms	51
Heterogen Atoms	64

Software

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

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.