1SZ2

Crystal structure of E. coli glucokinase in complex with glucose


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1Q18 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.5298PEG 6000, MgCl2, Tris-HCl buffer, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties
Matthews coefficientSolvent content
2.449.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.416α = 90
b = 53.538β = 112.99
c = 90.903γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42003-06-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X8C1.1NSLSX8C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
12.25089.50.05112.1318353183522
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.22.2863.40.1713.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1Q182.2503561630259160689.490.196890.196890.193410.26511RANDOM48.241
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]
-1.94-0.171.140.66
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.514
r_dihedral_angle_4_deg24.544
r_dihedral_angle_3_deg22.365
r_dihedral_angle_1_deg6.224
r_scangle_it3.896
r_scbond_it2.416
r_mcangle_it1.736
r_angle_refined_deg1.646
r_mcbond_it0.933
r_symmetry_hbond_refined0.691
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.514
r_dihedral_angle_4_deg24.544
r_dihedral_angle_3_deg22.365
r_dihedral_angle_1_deg6.224
r_scangle_it3.896
r_scbond_it2.416
r_mcangle_it1.736
r_angle_refined_deg1.646
r_mcbond_it0.933
r_symmetry_hbond_refined0.691
r_xyhbond_nbd_refined0.231
r_nbd_refined0.228
r_symmetry_vdw_refined0.144
r_chiral_restr0.117
r_bond_refined_d0.015
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4922
Nucleic Acid Atoms
Solvent Atoms348
Heterogen Atoms24

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
d*TREKdata scaling
MOLREPphasing