7WDN

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
3.3262.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 202.488α = 90
b = 202.488β = 90
c = 202.488γ = 90
Symmetry
Space GroupI 4 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2015-12-08MSINGLE 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
11.85099.90.06325.61361903
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)
11.81.830.637

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 REPLACEMENTTHROUGHOUT5XGZ1.83061901324199.950.161860.159340.21005RANDOM24.276
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.292
r_rigid_bond_restr7.741
r_dihedral_angle_1_deg6.768
r_scangle_other6.5
r_long_range_B_refined5.928
r_long_range_B_other5.893
r_scbond_other5.864
r_scbond_it5.863
r_mcangle_other3.958
r_mcangle_it3.956
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.292
r_rigid_bond_restr7.741
r_dihedral_angle_1_deg6.768
r_scangle_other6.5
r_long_range_B_refined5.928
r_long_range_B_other5.893
r_scbond_other5.864
r_scbond_it5.863
r_mcangle_other3.958
r_mcangle_it3.956
r_dihedral_angle_2_deg3.743
r_mcbond_it3.452
r_mcbond_other3.452
r_angle_refined_deg1.774
r_angle_other_deg0.744
r_chiral_restr0.077
r_bond_refined_d0.012
r_bond_other_d0.009
r_gen_planes_refined0.009
r_gen_planes_other0.007
r_dihedral_angle_4_deg
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 Atoms3644
Nucleic Acid Atoms
Solvent Atoms221
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing