2IM9

Crystal structure of protein LPG0564 from Legionella pneumophila str. Philadelphia 1, Pfam DUF1460

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7	294	3600mM sodium formate, pH 7, VAPOR DIFFUSION, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
1.92	35.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.892	α = 90
b = 71.052	β = 90
c = 83.904	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	77	CCD	ADSC QUANTUM 315		2006-09-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A	0.97958	NSLS	X29A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.67	20	89.8	0.063	0.063	19.3	6.2	34781	31234			17.9

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.67	1.76	45		0.265	0.265	2.6	2.1	4942

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	1.67	20	32931	29661	1566	90.07	0.17344	0.17151	0.21156	RANDOM	21.288

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]
1.69			-1.09		-0.6

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.007
r_dihedral_angle_4_deg	17.778
r_dihedral_angle_3_deg	12.698
r_dihedral_angle_1_deg	5.333
r_scangle_it	3.321
r_scbond_it	2.194
r_mcangle_it	1.356
r_angle_refined_deg	1.208
r_mcbond_it	0.828
r_nbtor_refined	0.311

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.007
r_dihedral_angle_4_deg	17.778
r_dihedral_angle_3_deg	12.698
r_dihedral_angle_1_deg	5.333
r_scangle_it	3.321
r_scbond_it	2.194
r_mcangle_it	1.356
r_angle_refined_deg	1.208
r_mcbond_it	0.828
r_nbtor_refined	0.311
r_symmetry_hbond_refined	0.251
r_symmetry_vdw_refined	0.203
r_xyhbond_nbd_refined	0.2
r_nbd_refined	0.199
r_chiral_restr	0.081
r_bond_refined_d	0.01
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2430
Nucleic Acid Atoms
Solvent Atoms	271
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
ADSC	data collection
DENZO	data reduction
SCALEPACK	data scaling
SHELXS	phasing

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.