3AAR | pdb_00003aar

Crystal structure of Lp1NTPDase from Legionella pneumophila in complex with AMPPNP

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3AAP	PDB ENTRY 3AAP

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	294	20-24%(w/v) PEG 3350, 0.2M Na Formate, 0.1M Bis-Tris propane pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.98	58.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 104.701	α = 90
b = 104.701	β = 90
c = 75.415	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	ADSC QUANTUM 210			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX1	0.954	Australian Synchrotron	MX1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.65	35	97.6	0.119	14.3	7.5		55849

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.65	1.74	98.8		0.452	3.5	7.3

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 3AAP	1.65	20	52982	2838	96.92	0.17753	0.17645	0.18	0.19717	0.2	RANDOM	17.487

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]
0.48	0.24		0.48		-0.72

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.835
r_dihedral_angle_4_deg	20.056
r_dihedral_angle_3_deg	12.365
r_dihedral_angle_1_deg	5.097
r_scangle_it	3.865
r_scbond_it	2.886
r_mcangle_it	1.758
r_mcbond_it	1.445
r_angle_refined_deg	1.26
r_chiral_restr	0.34

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.835
r_dihedral_angle_4_deg	20.056
r_dihedral_angle_3_deg	12.365
r_dihedral_angle_1_deg	5.097
r_scangle_it	3.865
r_scbond_it	2.886
r_mcangle_it	1.758
r_mcbond_it	1.445
r_angle_refined_deg	1.26
r_chiral_restr	0.34
r_nbtor_refined	0.31
r_symmetry_vdw_refined	0.215
r_nbd_refined	0.211
r_symmetry_hbond_refined	0.144
r_xyhbond_nbd_refined	0.136
r_metal_ion_refined	0.099
r_bond_refined_d	0.011
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2947
Nucleic Acid Atoms
Solvent Atoms	494
Heterogen Atoms	31

Software

Software
Software Name	Purpose
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

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.