3BHS | pdb_00003bhs

Nitrosomonas europaea Rh50 and mechanism of conduction by Rhesus protein family of channels

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2NS1	PDB entry 2NS1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	298	1:1 microliter drop ratio of (Protein in 0.02M HEPES pH 7.4, 0.1M NaCl, 0.04M B-octyl glucoside, 2mM Dithiothreitol) and (100mM HEPES, 25% PEG 400). Cryoprotected with 10% Glycerol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.91	57.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 96.675	α = 90
b = 96.675	β = 90
c = 137.621	γ = 120

Symmetry
Space Group	H 3

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	78	CCD	ADSC QUANTUM 4		2007-03-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1	1.11587	ALS	8.3.1

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	1.99	50	99.8	0.097	14.7	6.3		32561		2	23.8

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)
	1.99	2.07	98.2		0.395	2.4	3.1	3221

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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 2NS1	1.99	40.06	1	32561	30705	1646	98.9	0.19831	0.1963	0.19628	0.2	0.23666	0.24	RANDOM	27.769

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]
1.92	0.96		1.92		-2.88

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.356
r_dihedral_angle_3_deg	12.961
r_dihedral_angle_4_deg	11.362
r_dihedral_angle_1_deg	5.689
r_mcangle_it	3.736
r_scangle_it	3.554
r_mcbond_it	3.192
r_scbond_it	2.681
r_angle_refined_deg	1.487
r_mcbond_other	0.986
r_angle_other_deg	0.929
r_nbd_refined	0.245
r_symmetry_vdw_other	0.238
r_nbtor_refined	0.198
r_nbd_other	0.179
r_xyhbond_nbd_refined	0.167
r_symmetry_hbond_refined	0.151
r_chiral_restr	0.096
r_symmetry_vdw_refined	0.091
r_nbtor_other	0.088
r_xyhbond_nbd_other	0.068
r_bond_refined_d	0.017
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2806
Nucleic Acid Atoms
Solvent Atoms	154
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing