9JTG | pdb_00009jtg

Crystal Structure of 5'-Deoxy-5'-methylthioadenosine phosphorylase from Aeropyrum pernix 353K


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1WTA 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1COUNTER-DIFFUSION5.4293.2The mixture of protein solution and agarose was filled into a glass capillary, and the capillary was immersed in the reservoir solution for crystallization. The composition of the reservoir solution was as follows.15%(v/v)PEG#200,0.1 M phosphate citrate pH 5.4
Crystal Properties
Matthews coefficientSolvent content
2.28646.228

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.127α = 90
b = 79.127β = 90
c = 233.26γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray353PIXELDECTRIS EIGER X 16M2024-10-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-17A0.98Photon FactoryBL-17A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim 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
11.6844.411000.0680.0760.0330.99921.61032535
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.681.711000.9991.1150.490.6922.79.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)Mean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE1WTA1.6844.4132533159699.9230.1410.140.15110.16870.173828.816
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]
0.1020.0510.102-0.331
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg14.6
r_dihedral_angle_3_deg13.942
r_lrange_it10.341
r_lrange_other10.34
r_dihedral_angle_2_deg8.858
r_scangle_it8.335
r_scangle_other8.332
r_dihedral_angle_1_deg6.877
r_scbond_it5.267
r_scbond_other5.266
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg14.6
r_dihedral_angle_3_deg13.942
r_lrange_it10.341
r_lrange_other10.34
r_dihedral_angle_2_deg8.858
r_scangle_it8.335
r_scangle_other8.332
r_dihedral_angle_1_deg6.877
r_scbond_it5.267
r_scbond_other5.266
r_mcangle_it3.975
r_mcangle_other3.973
r_mcbond_it2.824
r_mcbond_other2.824
r_angle_refined_deg1.892
r_angle_other_deg0.638
r_nbd_refined0.215
r_nbd_other0.202
r_symmetry_nbd_other0.199
r_nbtor_refined0.179
r_symmetry_nbd_refined0.157
r_xyhbond_nbd_refined0.125
r_chiral_restr0.096
r_symmetry_xyhbond_nbd_refined0.09
r_symmetry_nbtor_other0.085
r_dihedral_angle_other_2_deg0.043
r_bond_refined_d0.011
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2142
Nucleic Acid Atoms
Solvent Atoms48
Heterogen Atoms15

Software

Software
Software NamePurpose
REFMACrefinement
Cootmodel building
MOLREPphasing
Aimlessdata scaling
XDSdata reduction