6DB1 | pdb_00006db1

2.0 Angstrom Resolution Crystal Structure of N-Terminal Ligand-Binding Domain of Putative Methyl-Accepting Chemotaxis Protein from Salmonella enterica

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	292	Protein: 7.0 mg/ml, 0.01M Tris HCl (pH 8.3), ATP, Mg, Screen: PACT (C5), 0.1 PCB buffer (pH 8.0), 25% (w/v) PEG 1500

Crystal Properties
Matthews coefficient	Solvent content
2.13	42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.226	α = 90
b = 89.226	β = 90
c = 65.89	γ = 120

Symmetry
Space Group	P 63

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	C(111)	2016-10-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97856	APS	21-ID-G

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	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	30	99.8	0.075	0.075	0.084	0.036	28.9	5.6		20259		-3	39.5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.03	100		0.826	0.826	0.926	0.415	0.718	2.04	4.9

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2	29.21	19193	1036	99.72	0.22438	0.22218	0.24	0.26448	0.28	RANDOM	52.644

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]
-1.82	-0.91		-1.82		5.91

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.185
r_dihedral_angle_3_deg	11.449
r_dihedral_angle_4_deg	9.993
r_long_range_B_refined	6.682
r_long_range_B_other	6.678
r_scangle_other	3.963
r_mcangle_it	3.252
r_mcangle_other	3.252
r_scbond_it	2.536
r_scbond_other	2.523
r_dihedral_angle_1_deg	2.211
r_mcbond_it	2.112
r_mcbond_other	2.111
r_angle_refined_deg	1.361
r_angle_other_deg	0.476
r_chiral_restr	0.066
r_gen_planes_refined	0.023
r_gen_planes_other	0.021
r_bond_refined_d	0.008
r_bond_other_d	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2109
Nucleic Acid Atoms
Solvent Atoms	81
Heterogen Atoms	1

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing