8WDG

Subatomic crystal structure of glucose isomerase from Streptomyces rubiginosus


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7CJP 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP295Tris-HCl, pH 8.0, PEG400, MgCl2
Crystal Properties
Matthews coefficientSolvent content
2.7254.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 92.675α = 90
b = 98.626β = 90
c = 102.137γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2021-12-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPAL/PLS BEAMLINE 11C0.8265PAL/PLS11C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)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
10.9940.7799.50.99912.26.1255970
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
10.991.0194.60.561

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT0.9940.772435321288399.50.158740.158120.17071RANDOM10.999
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]
0.010.42-0.43
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.957
r_dihedral_angle_4_deg13.805
r_dihedral_angle_3_deg11.187
r_dihedral_angle_1_deg6.098
r_long_range_B_refined4.745
r_long_range_B_other4.383
r_scangle_other3.397
r_scbond_it2.306
r_scbond_other2.306
r_angle_refined_deg2.043
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.957
r_dihedral_angle_4_deg13.805
r_dihedral_angle_3_deg11.187
r_dihedral_angle_1_deg6.098
r_long_range_B_refined4.745
r_long_range_B_other4.383
r_scangle_other3.397
r_scbond_it2.306
r_scbond_other2.306
r_angle_refined_deg2.043
r_angle_other_deg1.677
r_mcangle_other1.285
r_mcangle_it1.277
r_mcbond_it0.943
r_mcbond_other0.907
r_chiral_restr0.12
r_bond_refined_d0.018
r_gen_planes_refined0.013
r_gen_planes_other0.002
r_bond_other_d0.001
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 Atoms3033
Nucleic Acid Atoms
Solvent Atoms502
Heterogen Atoms13

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
MOLREPphasing