1NQH | pdb_00001nqh

OUTER MEMBRANE COBALAMIN TRANSPORTER (BTUB) FROM E. COLI, WITH BOUND CALCIUM AND CYANOCOBALAMIN (VITAMIN B12) SUBSTRATE

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.6	293	PEG 3350, MAGNESIUM ACETATE, BIS-TRIS, N-OCTYL TETRAOXYETHYLENE, pH 6.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.28	62.44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.687	α = 90
b = 81.687	β = 90
c = 225.814	γ = 120

Symmetry
Space Group	P 31 2 1

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 QUANTUM 315		2002-07-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X25	1.6037	NSLS	X25

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	3.1	20	99.9	0.07	28.2	6.3	30657	30643		-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	3.1	3.21	99.6		0.115	5.2	6.31	193476

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 Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT + SAD	THROUGHOUT	PDB ENTRY 1NQF	3.1	20	15703	15679	837	99.85	0.2259	0.2238	0.23	0.2646	RANDOM	23.448

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]
-0.91	-0.46		-0.91		1.37

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	25.749
r_dihedral_angle_1_deg	12.159
r_scangle_it	8.661
r_scbond_it	5.949
r_mcangle_it	3.632
r_angle_refined_deg	3.097
r_mcbond_it	2.238
r_angle_other_deg	1.259
r_chiral_restr	0.409
r_nbd_refined	0.391
r_nbd_other	0.366
r_symmetry_vdw_other	0.332
r_symmetry_vdw_refined	0.296
r_symmetry_hbond_refined	0.275
r_xyhbond_nbd_other	0.236
r_xyhbond_nbd_refined	0.234
r_nbtor_other	0.068
r_gen_planes_refined	0.043
r_bond_refined_d	0.032
r_gen_planes_other	0.018
r_bond_other_d	0.001
r_symmetry_hbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4630
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	223

Software

Software
Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
AMoRE	phasing
SHARP	phasing
REFMAC	refinement
HKL-2000	data reduction