1TZC

Crystal structure of phosphoglucose/phosphomannose isomerase from Pyrobaculum aerophilum in complex with 5-phosphoarabinonate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherNATIVE STRUCTURE

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 = 55.8α = 90
b = 100.85β = 113.7
c = 55.8γ = 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
11.453697.80.0780.07813.42.9979549795417.1
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)
11.451.594.30.4620.4621.62.59407

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 DIFFRACTIONREFINEMENT FROM NATIVE STRUCTURETHROUGHOUTNATIVE STRUCTURE1.45369773697736486694.20.170.170.1690.192RANDOM15.34
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]
-0.37-0.26-0.040.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.827
r_scangle_it3.147
r_scbond_it1.829
r_angle_refined_deg1.273
r_mcangle_it1.099
r_angle_other_deg1.091
r_mcbond_it0.586
r_symmetry_vdw_other0.257
r_nbd_other0.233
r_nbd_refined0.209
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.827
r_scangle_it3.147
r_scbond_it1.829
r_angle_refined_deg1.273
r_mcangle_it1.099
r_angle_other_deg1.091
r_mcbond_it0.586
r_symmetry_vdw_other0.257
r_nbd_other0.233
r_nbd_refined0.209
r_symmetry_hbond_refined0.144
r_xyhbond_nbd_refined0.13
r_symmetry_vdw_refined0.104
r_nbtor_other0.081
r_chiral_restr0.079
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4717
Nucleic Acid Atoms
Solvent Atoms439
Heterogen Atoms67

Software

Software
Software NamePurpose
REFMACrefinement
MAR345data collection
SCALEPACKdata scaling