2NPK | pdb_00002npk

An unusual twin-His arrangement in the pore of ammonia channels is essential for substrate conductance

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1XQF	PDB ENTRY 1XQF

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.6	298	30% PEG 400, 0.1M SODIUM ACETATE, 0.2M AMMONIUM SULFATE, PH 4.6, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K, pH 4.60

Crystal Properties
Matthews coefficient	Solvent content
3.3	62.77

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 109.917	α = 90
b = 109.917	β = 90
c = 84.203	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 225 mm CCD		2006-03-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	0.97934	SLS	X06SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2	50	99.8	0.086	18.24			39048		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.1	99.9		0.75	3.12

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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 1XQF	2	15	39019	37020	1955	99.89	0.16631	0.16502	0.21	0.19031	0.23	RANDOM	41.21

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]
1.36	0.68		1.36		-2.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.427
r_dihedral_angle_4_deg	15.723
r_dihedral_angle_3_deg	13.954
r_scangle_it	3.879
r_scbond_it	2.793
r_mcangle_it	1.806
r_dihedral_angle_1_deg	1.719
r_angle_refined_deg	1.362
r_mcbond_it	1.127
r_nbtor_refined	0.311
r_xyhbond_nbd_refined	0.27
r_nbd_refined	0.205
r_symmetry_hbond_refined	0.169
r_symmetry_vdw_refined	0.147
r_chiral_restr	0.106
r_bond_refined_d	0.011
r_gen_planes_refined	0.008
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2741
Nucleic Acid Atoms
Solvent Atoms	118
Heterogen Atoms	25

Software

Software
Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
MAR345	data collection
XDS	data reduction
XSCALE	data scaling