3C9J

The Crystal structure of Transmembrane domain of M2 protein and Amantadine complex


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelOtherPolyala, single alpha helix of length 23 residues

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.3298Sample solution: 0.8mM protein, 0.6mM Amantadine, 32mM n-octyl-beta-D-glucopyranoside and 5% w/v Xylitol. Reservoir solution:50mM Tris-Hcl, 500mM MgCl2, 30mM NiCl2, 22% PEG 350 MME, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties
Matthews coefficientSolvent content
3.0359.42

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.397α = 90
b = 57.833β = 90
c = 38.105γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plateOsmic mirrors2004-12-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
13.51592.40.10512.34.219991848-363.1
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.53.611000.3623.13.7163

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPolyala, single alpha helix of length 23 residues3.515153015491.270.293220.290540.31668RANDOM35.151
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]
0.46-2.021.56
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.455
r_dihedral_angle_3_deg20.118
r_dihedral_angle_4_deg14.353
r_dihedral_angle_1_deg3.541
r_angle_refined_deg2.165
r_scangle_it1.165
r_scbond_it0.651
r_mcangle_it0.432
r_mcbond_it0.396
r_nbtor_refined0.362
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.455
r_dihedral_angle_3_deg20.118
r_dihedral_angle_4_deg14.353
r_dihedral_angle_1_deg3.541
r_angle_refined_deg2.165
r_scangle_it1.165
r_scbond_it0.651
r_mcangle_it0.432
r_mcbond_it0.396
r_nbtor_refined0.362
r_symmetry_vdw_refined0.355
r_nbd_refined0.334
r_symmetry_hbond_refined0.243
r_xyhbond_nbd_refined0.16
r_chiral_restr0.11
r_bond_refined_d0.029
r_gen_planes_refined0.01
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 AtomsNumber
Protein Atoms772
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms11

Software

Software
Software NamePurpose
MAR345dtbdata collection
PHASERphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling