8QK8 | pdb_00008qk8

Structure of Legionella pneumophila Lcl C-terminal domain bound to sulphate

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		Lcl-CTD

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	293	20% (v/v) glycerol, 20% (w/v) polyethylene glycol (PEG) 4000, 30 mM NaNO3, 30 mM Na2HPO4, 30 mM (NH4)2SO4, 100 mM bicine, 100 mM tris-HCl

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.91	α = 90
b = 74.91	β = 90
c = 94.97	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	PIXEL	DECTRIS PILATUS 6M-F		2015-01-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97625	Diamond	I03

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	1.9	64.91	100	0.074	28.7	19.3		24856			24.7

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	1.9	1.93	99.8		0.541	5.8	14.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.9	64.874	24854	1200	99.968	0.162	0.1604	0.17	0.1874	0.2	25.968

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]
0.222	0.111		0.222		-0.721

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.377
r_dihedral_angle_3_deg	13.454
r_dihedral_angle_1_deg	6.799
r_lrange_it	6.791
r_lrange_other	6.726
r_scangle_it	5.743
r_scangle_other	5.714
r_dihedral_angle_2_deg	5.635
r_scbond_it	3.831
r_scbond_other	3.811
r_mcangle_it	3.138
r_mcangle_other	3.138
r_mcbond_it	2.227
r_mcbond_other	2.226
r_angle_refined_deg	1.462
r_angle_other_deg	0.761
r_nbd_other	0.232
r_symmetry_nbd_other	0.205
r_nbd_refined	0.198
r_nbtor_refined	0.18
r_symmetry_nbd_refined	0.168
r_xyhbond_nbd_refined	0.165
r_symmetry_xyhbond_nbd_refined	0.158
r_symmetry_nbtor_other	0.085
r_ncsr_local_group_1	0.073
r_chiral_restr	0.065
r_gen_planes_other	0.01
r_bond_refined_d	0.008
r_gen_planes_refined	0.008
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2058
Nucleic Acid Atoms
Solvent Atoms	194
Heterogen Atoms	10

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing