7WDS

Crystal structures of MeBglD2 in complex with various saccharides


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5XGZ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2930.1 M Tris-HCl buffer (pH 8.5), 1.2 M lithium sulfate, 0.01 M nickel chloride
Crystal Properties
Matthews coefficientSolvent content
3.3563.26

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 203.169α = 90
b = 203.169β = 90
c = 203.169γ = 90
Symmetry
Space GroupI 4 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300HE2016-05-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL44XU0.9SPring-8BL44XU

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
11.685099.90.09827.819.380168
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)
11.681.710.745

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 REPLACEMENTTHROUGHOUT5XGZ1.6841.4776179391899.980.168470.165360.22864RANDOM29.144
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]
7.43-10.71-28.8123.19-13.27-30.62
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.521
r_dihedral_angle_4_deg16.285
r_dihedral_angle_3_deg14.633
r_scangle_other7.354
r_dihedral_angle_1_deg6.974
r_scbond_it6.667
r_long_range_B_refined6.58
r_long_range_B_other6.563
r_scbond_other6.531
r_rigid_bond_restr4.299
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.521
r_dihedral_angle_4_deg16.285
r_dihedral_angle_3_deg14.633
r_scangle_other7.354
r_dihedral_angle_1_deg6.974
r_scbond_it6.667
r_long_range_B_refined6.58
r_long_range_B_other6.563
r_scbond_other6.531
r_rigid_bond_restr4.299
r_mcangle_it4.195
r_mcangle_other4.195
r_mcbond_it3.64
r_mcbond_other3.639
r_angle_refined_deg1.975
r_angle_other_deg1.493
r_chiral_restr0.094
r_bond_refined_d0.014
r_gen_planes_refined0.012
r_bond_other_d0.002
r_gen_planes_other0.001
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_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3596
Nucleic Acid Atoms
Solvent Atoms294
Heterogen Atoms30

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing