3PUY

Crystal Structure of an outward-facing MBP-Maltose transporter complex bound to AMP-PNP after crystal soaking of the pretranslocation state


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2R6Gpdb entry 2R6G

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.529332% PEG 400, 0.1 M HEPES, 40 mM magnesium chloride, 50 mM sodium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 293K, pH 7.5
Crystal Properties
Matthews coefficientSolvent content
3.6566.34

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 76.55α = 86.91
b = 96.283β = 80.87
c = 112.283γ = 74.32
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2009-05-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-D1.03324APS23-ID-D

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
12.82064.90.0614661346613
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)
12.82.923.90.5321.31.5

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 REPLACEMENTTHROUGHOUTpdb entry 2R6G3.1204661343231230182.690.216290.214260.25427RANDOM81.172
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]
-0.560.210.190.63-0.2-0.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.357
r_dihedral_angle_3_deg17.059
r_dihedral_angle_4_deg16.953
r_dihedral_angle_1_deg4.655
r_angle_refined_deg1.011
r_scangle_it0.815
r_mcangle_it0.463
r_scbond_it0.45
r_mcbond_it0.248
r_chiral_restr0.065
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.357
r_dihedral_angle_3_deg17.059
r_dihedral_angle_4_deg16.953
r_dihedral_angle_1_deg4.655
r_angle_refined_deg1.011
r_scangle_it0.815
r_mcangle_it0.463
r_scbond_it0.45
r_mcbond_it0.248
r_chiral_restr0.065
r_bond_refined_d0.006
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
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 Atoms14640
Nucleic Acid Atoms
Solvent Atoms11
Heterogen Atoms138

Software

Software
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling