6JAD

Crystal structure of ABC transporter alpha-glycoside-binding protein in complex with palatinose


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6J9W 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH52770.05 M Citric Acid, 0.05 M Bis-Tris Propane, 16% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.8757.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 84.77α = 90
b = 84.77β = 90
c = 145.83γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++VariMax HF2018-02-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
11.973.2999.90.0830.0970.050.99713.26.642666
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.99.1199.60.4490.5240.2680.9153.66.9

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 REPLACEMENTTHROUGHOUT6J9W1.973.2940512209799.90.14150.13940.1816RANDOM22.409
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]
0.840.84-1.68
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.738
r_dihedral_angle_4_deg15.486
r_dihedral_angle_3_deg13.363
r_dihedral_angle_1_deg5.852
r_angle_refined_deg1.804
r_angle_other_deg0.902
r_chiral_restr0.116
r_bond_refined_d0.018
r_gen_planes_refined0.011
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.738
r_dihedral_angle_4_deg15.486
r_dihedral_angle_3_deg13.363
r_dihedral_angle_1_deg5.852
r_angle_refined_deg1.804
r_angle_other_deg0.902
r_chiral_restr0.116
r_bond_refined_d0.018
r_gen_planes_refined0.011
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3227
Nucleic Acid Atoms
Solvent Atoms517
Heterogen Atoms49

Software

Software
Software NamePurpose
HKL-3000data collection
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
REFMACrefinement
Cootmodel building
PDB_EXTRACTdata extraction