1X9H

Crystal structure of phosphoglucose/phosphomannose isomerase from Pyrobaculum aerophilum in complex with fructose 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 = 55.2α = 90
b = 100.8β = 113.4
c = 55.9γ = 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
11.53696.80.0630.06319.53.6867578675716.1
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)
11.51.5582.80.3910.3911.72.87410

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 1TZB1.5368750886508429096.380.1530.1530.1520.18RANDOM16.35
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]
0.95-0.48-0.42-0.91
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.626
r_dihedral_angle_4_deg17.125
r_dihedral_angle_3_deg13.52
r_dihedral_angle_1_deg5.124
r_sphericity_free3.886
r_rigid_bond_restr3.275
r_scangle_it2.854
r_scbond_it2.297
r_sphericity_bonded1.466
r_angle_refined_deg1.343
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.626
r_dihedral_angle_4_deg17.125
r_dihedral_angle_3_deg13.52
r_dihedral_angle_1_deg5.124
r_sphericity_free3.886
r_rigid_bond_restr3.275
r_scangle_it2.854
r_scbond_it2.297
r_sphericity_bonded1.466
r_angle_refined_deg1.343
r_mcangle_it1.192
r_angle_other_deg1.128
r_mcbond_it0.991
r_mcbond_other0.268
r_symmetry_vdw_other0.267
r_nbd_refined0.212
r_nbd_other0.182
r_symmetry_hbond_refined0.182
r_nbtor_refined0.176
r_xyhbond_nbd_refined0.144
r_symmetry_vdw_refined0.112
r_nbtor_other0.082
r_chiral_restr0.075
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4716
Nucleic Acid Atoms
Solvent Atoms403
Heterogen Atoms81

Software

Software
Software NamePurpose
REFMACrefinement
MAR345data collection
SCALEPACKdata scaling