1X9I

Crystal structure of Crystal structure of phosphoglucose/phosphomannose phosphoglucose/phosphomannoseisomerase from Pyrobaculum aerophilum in complex with glucose 6-phosphate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1TZBpdb entry 1tzb

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.529525% polyethylene glycol 8000, 0.22M ammonium sulphate, 100mM Tris, pH 8.5 , VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.142

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.9α = 90
b = 100.8β = 113.8
c = 56.1γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2003-10-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1.00APS22-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.1636900.0490.049407.117610917610910
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.161.277.50.2330.23344.915133

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 DIFFRACTIONrefinementTHROUGHOUTpdb entry 1tzb1.1636176101176101887190.010.1480.1480.1470.164RANDOM12.014
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]
0.26-0.380.26-0.84
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.956
r_dihedral_angle_4_deg14.584
r_dihedral_angle_3_deg11.855
r_dihedral_angle_1_deg5.32
r_sphericity_free3.974
r_sphericity_bonded2.575
r_scangle_it2.496
r_scbond_it1.884
r_angle_refined_deg1.333
r_mcangle_it1.297
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.956
r_dihedral_angle_4_deg14.584
r_dihedral_angle_3_deg11.855
r_dihedral_angle_1_deg5.32
r_sphericity_free3.974
r_sphericity_bonded2.575
r_scangle_it2.496
r_scbond_it1.884
r_angle_refined_deg1.333
r_mcangle_it1.297
r_mcbond_it1.076
r_rigid_bond_restr0.995
r_angle_other_deg0.881
r_mcbond_other0.451
r_nbd_refined0.214
r_symmetry_vdw_other0.211
r_nbd_other0.183
r_symmetry_vdw_refined0.18
r_nbtor_refined0.174
r_xyhbond_nbd_refined0.117
r_symmetry_hbond_refined0.092
r_chiral_restr0.083
r_nbtor_other0.083
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_gen_planes_other0.003
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4707
Nucleic Acid Atoms
Solvent Atoms559
Heterogen Atoms44

Software

Software
Software NamePurpose
REFMACrefinement
MAR345data collection
SCALEPACKdata scaling