9IX8

Crystallization and structural characterization of phosphopentomutase from the hyperthermophilic archaeon Thermococcus kodakarensis


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelAlphaFoldAF-Q6I7B6-F1 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29320% v/v PEG300, 10% v/v Glycerol, 0.1 M Tris-HCl- pH 8.5, 5% w/v PEG8000
Crystal Properties
Matthews coefficientSolvent content
2.5151.08

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.772α = 90
b = 97.575β = 94
c = 128.15γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 4M2023-11-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-1A1.90Photon FactoryBL-1A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)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
12.395098.90.1250.1350.99810.48777057
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.392.53971.0390.50.71.576.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.395074699231099.010.20330.201110.27378RANDOM50.494
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]
0.520.530.49-1.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.996
r_dihedral_angle_4_deg20.915
r_dihedral_angle_3_deg19.151
r_long_range_B_other10.838
r_long_range_B_refined10.833
r_dihedral_angle_1_deg8.012
r_scangle_other7.916
r_mcangle_other6.676
r_mcangle_it6.675
r_scbond_it5.222
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.996
r_dihedral_angle_4_deg20.915
r_dihedral_angle_3_deg19.151
r_long_range_B_other10.838
r_long_range_B_refined10.833
r_dihedral_angle_1_deg8.012
r_scangle_other7.916
r_mcangle_other6.676
r_mcangle_it6.675
r_scbond_it5.222
r_scbond_other5.221
r_mcbond_it4.612
r_mcbond_other4.608
r_angle_refined_deg1.721
r_angle_other_deg1.266
r_chiral_restr0.081
r_bond_refined_d0.01
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms13803
Nucleic Acid Atoms
Solvent Atoms419
Heterogen Atoms48

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata scaling
PHASERphasing
XDSdata reduction