5Y4J

Crystal structure of glucose isomerase in complex with xylitol inhibitor in one metal binding mode


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1MNZ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP295.516% (w/v) PEG400 and 100 mM MgCl2
Crystal Properties
Matthews coefficientSolvent content
2.7455.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 92.614α = 90
b = 99.416β = 90
c = 102.019γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102017-05-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPAL/PLS BEAMLINE 7A (6B, 6C1)0.97950PAL/PLS7A (6B, 6C1)

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.42097.421.513.890133

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 REPLACEMENTTHROUGHOUT1MNZ1.419.9385616451697.150.15580.15450.1799RANDOM13.255
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]
0.030.03-0.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.938
r_dihedral_angle_4_deg14.978
r_dihedral_angle_3_deg11.676
r_dihedral_angle_1_deg5.69
r_angle_refined_deg2.451
r_angle_other_deg1.017
r_chiral_restr0.152
r_bond_refined_d0.027
r_gen_planes_refined0.014
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.938
r_dihedral_angle_4_deg14.978
r_dihedral_angle_3_deg11.676
r_dihedral_angle_1_deg5.69
r_angle_refined_deg2.451
r_angle_other_deg1.017
r_chiral_restr0.152
r_bond_refined_d0.027
r_gen_planes_refined0.014
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3022
Nucleic Acid Atoms
Solvent Atoms566
Heterogen Atoms11

Software

Software
Software NamePurpose
HKL-2000data collection
HKL-2000data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
MOLREPphasing