5AVH

The 0.90 angstrom structure (I222) of glucose isomerase crystallized in high-strength agarose hydrogel


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH72930.1M Tris-HCl (pH 7.0), 10% (v/v) MPD, 0.1M Ca acetate
Crystal Properties
Matthews coefficientSolvent content
2.7154.54

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 93.268α = 90
b = 97.588β = 90
c = 102.49γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS V2008-07-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL38B10.70000SPring-8BL38B1

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
10.95095.10.07311.63325304
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)
10.90.9294.30.3542.382.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONTHROUGHOUT0.9503000001600095.110.116830.116280.12735RANDOM9.067
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]
0.060.13-0.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.326
r_sphericity_free17.766
r_dihedral_angle_4_deg17.25
r_dihedral_angle_3_deg11.994
r_rigid_bond_restr11.59
r_dihedral_angle_1_deg5.823
r_sphericity_bonded5.589
r_long_range_B_refined2.42
r_angle_other_deg2.328
r_scangle_other2.182
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.326
r_sphericity_free17.766
r_dihedral_angle_4_deg17.25
r_dihedral_angle_3_deg11.994
r_rigid_bond_restr11.59
r_dihedral_angle_1_deg5.823
r_sphericity_bonded5.589
r_long_range_B_refined2.42
r_angle_other_deg2.328
r_scangle_other2.182
r_angle_refined_deg2.122
r_long_range_B_other1.954
r_scbond_it1.913
r_scbond_other1.905
r_mcangle_other1.001
r_mcangle_it0.976
r_mcbond_it0.849
r_mcbond_other0.828
r_chiral_restr0.123
r_bond_refined_d0.023
r_gen_planes_refined0.014
r_gen_planes_other0.011
r_bond_other_d0.002
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3042
Nucleic Acid Atoms
Solvent Atoms515
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
HKL-2000data scaling
MOLREPphasing