2I22

Crystal structure of Escherichia coli phosphoheptose isomerase in complex with reaction substrate sedoheptulose 7-phosphate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1TK9PDB entry 1TK9

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.32983% PEG 8000, 0.002 M DTT, 3% 1,6-hexanediol, 0.01 M Hepes, 0.1 M imidazole, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.2946.28

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.045α = 90
b = 76.54β = 106.13
c = 78.316γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2005-05-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU3001.5418

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
12.7947.3998.6205332053311
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.792.8999.4

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 1TK92.825188071880714781000.206940.202970.25699RANDOM44.337
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]
0.21-0.51-0.34-0.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.003
r_dihedral_angle_4_deg24.483
r_dihedral_angle_3_deg20.234
r_dihedral_angle_1_deg6.752
r_scangle_it5.438
r_scbond_it3.83
r_mcangle_it2.853
r_angle_refined_deg2.845
r_mcbond_it2.039
r_nbtor_refined0.35
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.003
r_dihedral_angle_4_deg24.483
r_dihedral_angle_3_deg20.234
r_dihedral_angle_1_deg6.752
r_scangle_it5.438
r_scbond_it3.83
r_mcangle_it2.853
r_angle_refined_deg2.845
r_mcbond_it2.039
r_nbtor_refined0.35
r_nbd_refined0.301
r_symmetry_vdw_refined0.243
r_xyhbond_nbd_refined0.221
r_chiral_restr0.187
r_symmetry_hbond_refined0.178
r_bond_refined_d0.038
r_gen_planes_refined0.011
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5436
Nucleic Acid Atoms
Solvent Atoms211
Heterogen Atoms18

Software

Software
Software NamePurpose
REFMACrefinement
CrystalCleardata collection
CrystalCleardata reduction
CrystalCleardata scaling
CNSphasing