1NUH

The crystal structure of human phosphoglucose isomerase complexed with 5-phosphoarabinonate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1IATPDN ENTRY 1IAT

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.52942.1 M ammonium sulphate, 100 mM Tris pH 8.5, 5 mM 5-phosphoarabinonate, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
2.4149.06

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 94.4α = 90
b = 94.4β = 90
c = 137.1γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IVOsmic mirrors2000-12-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU3001.5418

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
12.5194.498.40.1280.1285.76.9217972179725.4
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)
12.512.5999.80.2540.2543.16.82171

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 DIFFRACTIONREFINEMENTTHROUGHOUTPDN ENTRY 1IAT2.51502146821468110198.40.2170.2170.2140.268RANDOM25.156
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]
-0.51-0.511.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg17.246
r_dihedral_angle_1_deg3.624
r_scangle_it3.022
r_scbond_it1.834
r_angle_refined_deg1.473
r_mcangle_it1.008
r_mcbond_it0.516
r_symmetry_hbond_refined0.348
r_nbd_refined0.241
r_symmetry_vdw_refined0.202
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg17.246
r_dihedral_angle_1_deg3.624
r_scangle_it3.022
r_scbond_it1.834
r_angle_refined_deg1.473
r_mcangle_it1.008
r_mcbond_it0.516
r_symmetry_hbond_refined0.348
r_nbd_refined0.241
r_symmetry_vdw_refined0.202
r_xyhbond_nbd_refined0.174
r_chiral_restr0.104
r_bond_refined_d0.011
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4424
Nucleic Acid Atoms
Solvent Atoms109
Heterogen Atoms45

Software

Software
Software NamePurpose
REFMACrefinement
CrystalCleardata reduction
CrystalCleardata scaling