4LUK

The crystal structure of the P132A, Y133G mutant of Pyrococcus furiosus phosphoglucose isomerase in complex with manganese and 5-phospho-D-arabinonate.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1X7NPDB ENTRY 1X7N

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.52900.35 M MgCl2, 0.1 M sodium acetate PH 5.5 and 19% PEG4000, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties
Matthews coefficientSolvent content
2.1843.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 87.85α = 90
b = 43.28β = 122.9
c = 58.45γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MDiamond IO32011-05-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.97630DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.4128.9291.20.036133.13279732797
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.411.4455.40.3492.12.41460

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 1X7N1.4128.92327973113416631000.153360.150090.21388RANDOM26.299
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]
-1.79-1.832.35-2.56
RMS Deviations
KeyRefinement Restraint Deviation
r_scbond_it86.29
r_scangle_it78.163
r_rigid_bond_restr52.302
r_mcbond_it37.221
r_mcangle_it35.504
r_dihedral_angle_2_deg29.068
r_mcbond_other21.17
r_dihedral_angle_4_deg12.722
r_dihedral_angle_3_deg10.587
r_dihedral_angle_1_deg5.954
RMS Deviations
KeyRefinement Restraint Deviation
r_scbond_it86.29
r_scangle_it78.163
r_rigid_bond_restr52.302
r_mcbond_it37.221
r_mcangle_it35.504
r_dihedral_angle_2_deg29.068
r_mcbond_other21.17
r_dihedral_angle_4_deg12.722
r_dihedral_angle_3_deg10.587
r_dihedral_angle_1_deg5.954
r_angle_refined_deg1.064
r_angle_other_deg0.726
r_chiral_restr0.063
r_bond_refined_d0.006
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1510
Nucleic Acid Atoms
Solvent Atoms195
Heterogen Atoms32

Software

Software
Software NamePurpose
GDAdata collection
PHASERphasing
REFMACrefinement
xia2data reduction
xia2data scaling