2J9D

Structure of GlnK1 with bound effectors indicates regulatory mechanism for ammonia uptake

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2J9C	PDB ENTRY 2J9C

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.5		pH 7.50

Crystal Properties
Matthews coefficient	Solvent content
2.17	43.41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 96.6	α = 90
b = 107.03	β = 90
c = 134.34	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	100	CCD	ADSC CCD		2004-05-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-1		ESRF	ID14-1

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	2.1	20	99	0.16	11.3	4.6		80980		3

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	2.1	2.2	98.8		0.53	3.06	4.6

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2J9C	2.1	19.78	76930	4050	100	0.21	0.207	0.265	RANDOM	30.31

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]
0.77			0.58		-1.35

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.328
r_dihedral_angle_4_deg	17.293
r_dihedral_angle_3_deg	17.209
r_dihedral_angle_1_deg	6.954
r_scangle_it	4.835
r_scbond_it	3.477
r_mcangle_it	2.673
r_mcbond_it	2.279
r_angle_refined_deg	1.446
r_angle_other_deg	0.944
r_symmetry_vdw_other	0.304
r_symmetry_vdw_refined	0.259
r_nbd_refined	0.212
r_nbd_other	0.207
r_xyhbond_nbd_refined	0.171
r_nbtor_refined	0.164
r_symmetry_hbond_refined	0.132
r_nbtor_other	0.085
r_chiral_restr	0.079
r_bond_refined_d	0.013
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9994
Nucleic Acid Atoms
Solvent Atoms	694
Heterogen Atoms	152

Software

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