5ZYE

Crystal Structure of Glucose Isomerase Soaked with Mn2+ and Glucose


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5Y4I 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP293.5PEG 400, MgCl2
Crystal Properties
Matthews coefficientSolvent content
2.7555.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 92.749α = 90
b = 98.961β = 90
c = 102.481γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2702017-09-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPAL/PLS BEAMLINE 7A (6B, 6C1)0.987PAL/PLS7A (6B, 6C1)

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
11.471.1993.70.0650.0860.0430.14.386795
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)
11.41.4298.80.3380.4980.230.94.434.2

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 REPLACEMENTTHROUGHOUT5Y4I1.471.1981908433693.070.168070.167150.18552RANDOM14.728
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]
-0.340.68-0.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.408
r_dihedral_angle_4_deg12.305
r_dihedral_angle_3_deg11.117
r_dihedral_angle_1_deg5.61
r_long_range_B_refined4.922
r_long_range_B_other4.706
r_scangle_other3.608
r_scbond_it2.406
r_scbond_other2.406
r_angle_refined_deg2.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.408
r_dihedral_angle_4_deg12.305
r_dihedral_angle_3_deg11.117
r_dihedral_angle_1_deg5.61
r_long_range_B_refined4.922
r_long_range_B_other4.706
r_scangle_other3.608
r_scbond_it2.406
r_scbond_other2.406
r_angle_refined_deg2.06
r_mcangle_other1.789
r_mcangle_it1.778
r_mcbond_it1.288
r_mcbond_other1.249
r_angle_other_deg1.175
r_chiral_restr0.132
r_bond_refined_d0.021
r_gen_planes_refined0.012
r_bond_other_d0.001
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3022
Nucleic Acid Atoms
Solvent Atoms457
Heterogen Atoms14

Software

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