5TU0

1.9 Angstrom Resolution Crystal Structure of Maltose-Binding Periplasmic Protein MalE from Listeria monocytogenes in Complex with Maltose


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2XD3 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP295Protein: 15.2 mg/ml, 0.5M Sodium chloride, 0.01M Tris HCl (pH 8.3), 2mM MAL; Screen: Classics II (C2), 1.1M Ammonium tartrate (pH 7.0).
Crystal Properties
Matthews coefficientSolvent content
2.3647.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.208α = 90
b = 78.452β = 90
c = 90.69γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDC(111)2016-10-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.97856APS21-ID-G

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.9301000.0810.08134.4733694-329.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.91.931000.7790.8262.96.8

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 REPLACEMENTTHROUGHOUT2XD31.929.6731867155799.940.176030.174360.20823RANDOM33.167
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]
-2.250.212.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.263
r_dihedral_angle_4_deg10.16
r_dihedral_angle_3_deg9.657
r_long_range_B_refined5.345
r_long_range_B_other5.227
r_dihedral_angle_1_deg3.12
r_scangle_other2.411
r_scbond_it1.508
r_scbond_other1.504
r_mcangle_it1.494
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.263
r_dihedral_angle_4_deg10.16
r_dihedral_angle_3_deg9.657
r_long_range_B_refined5.345
r_long_range_B_other5.227
r_dihedral_angle_1_deg3.12
r_scangle_other2.411
r_scbond_it1.508
r_scbond_other1.504
r_mcangle_it1.494
r_mcangle_other1.493
r_angle_refined_deg1.339
r_mcbond_it0.943
r_mcbond_other0.943
r_angle_other_deg0.866
r_chiral_restr0.089
r_gen_planes_refined0.023
r_gen_planes_other0.019
r_bond_refined_d0.009
r_bond_other_d0.001
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3007
Nucleic Acid Atoms
Solvent Atoms284
Heterogen Atoms41

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing