Experiment: 6NFE

Crystal Structure of Ribose-phosphate Pyrophosphokinase from Legionella pneumophila with bound AMP, ADP, and Ribose-5-Phosphate

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4S2U

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.2	290	LepnA.00035.a.B1.PS38405 at 19.13 mg/ml was incubated with 4 mM ribose-5-phosphate, 4 mM ATP, and 4 mM MgCl2 then was mixed 1:1 JCSG+(b6): 40% (v/v) reagent alcohol, 100 mM sodium phosphate dibasic/citric acid pH 4.2. Tray: 298764b6, puck: uya9-9.

Crystal Properties
Matthews coefficient	Solvent content
2.37	48.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 109	α = 90
b = 109	β = 90
c = 97.3	γ = 120

Symmetry
Space Group	P 3 2 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 MX-300	Beryllium Lenses	2018-04-12	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	1.75	43.245	99.9	0.072	0.077	0.998	18.78	7.462		67559			26.218

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	1.75	1.8	100		0.455	0.491	0.916	5.38	7.462

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-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	4S2U	1.75	43.245	1.36	67554	1927	99.92	0.1525	0.1518	0.1764	0.1855	25.2569

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	4468
Nucleic Acid Atoms
Solvent Atoms	535
Heterogen Atoms	204

Software

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