1NQH

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1NQFPDB ENTRY 1NQF

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.6293PEG 3350, MAGNESIUM ACETATE, BIS-TRIS, N-OCTYL TETRAOXYETHYLENE, pH 6.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.2862.44

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.687α = 90
b = 81.687β = 90
c = 225.814γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152002-07-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X251.6037NSLSX25

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
13.12099.90.0728.26.33065730643-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.13.2199.60.1155.26.31193476

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENT + SADTHROUGHOUTPDB ENTRY 1NQF3.120157031567983799.850.22590.22380.2646RANDOM23.448
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]
-0.91-0.46-0.911.37
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg25.749
r_dihedral_angle_1_deg12.159
r_scangle_it8.661
r_scbond_it5.949
r_mcangle_it3.632
r_angle_refined_deg3.097
r_mcbond_it2.238
r_angle_other_deg1.259
r_chiral_restr0.409
r_nbd_refined0.391
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg25.749
r_dihedral_angle_1_deg12.159
r_scangle_it8.661
r_scbond_it5.949
r_mcangle_it3.632
r_angle_refined_deg3.097
r_mcbond_it2.238
r_angle_other_deg1.259
r_chiral_restr0.409
r_nbd_refined0.391
r_nbd_other0.366
r_symmetry_vdw_other0.332
r_symmetry_vdw_refined0.296
r_symmetry_hbond_refined0.275
r_xyhbond_nbd_other0.236
r_xyhbond_nbd_refined0.234
r_nbtor_other0.068
r_gen_planes_refined0.043
r_bond_refined_d0.032
r_gen_planes_other0.018
r_bond_other_d0.001
r_symmetry_hbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4630
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms223

Software

Software
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
SHARPphasing
REFMACrefinement
HKL-2000data reduction