2NPD | pdb_00002npd

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 550, 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 = 109.305	α = 90
b = 109.305	β = 90
c = 84.404	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		2005-11-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	0.98017	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	2.1	50	99.2	0.069	14.86			33268		-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	2.1	2.2	99.7		0.564	3.55

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 (All)	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	2.1	15	33439	31547	1683	99.37	0.17324	0.17324	0.17197	0.22	0.19787	0.24	RANDOM	46.932

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]
2.55	1.27		2.55		-3.82

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.602
r_dihedral_angle_4_deg	21.62
r_dihedral_angle_3_deg	14.76
r_scangle_it	4.923
r_scbond_it	3.554
r_mcangle_it	2.342
r_dihedral_angle_1_deg	1.819
r_angle_refined_deg	1.526
r_mcbond_it	1.509
r_nbtor_refined	0.322
r_nbd_refined	0.217
r_symmetry_vdw_refined	0.168
r_xyhbond_nbd_refined	0.119
r_chiral_restr	0.118
r_symmetry_hbond_refined	0.105
r_bond_refined_d	0.013
r_gen_planes_refined	0.009
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	2685
Nucleic Acid Atoms
Solvent Atoms	40
Heterogen Atoms	9

Software

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