9JHV

Crystal Structure of 5'-Deoxy-5'-methylthioadenosine phosphorylase from Aeropyrum pernix complex with 5'-Deoxy-5'-methylthioadenosine 343K


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1COUNTER-DIFFUSION293.2he 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, 5 mM MTA
Crystal Properties
Matthews coefficientSolvent content
2.2713645.8812599

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.854α = 90
b = 78.854β = 90
c = 233.369γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray343PIXELDECTRIS EIGER X 16M2024-06-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-17A1.0Photon 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
11.6544.361000.1410.1570.0680.997101034102
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)
1.651.681002.4692.7521.2030.3391.110

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-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE1WTA1.6544.3634101178899.9530.1210.11820.167428.908
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]
-0.329-0.165-0.3291.067
RMS Deviations
KeyRefinement Restraint Deviation
r_lrange_it19.605
r_lrange_other19.601
r_scangle_it16.426
r_scangle_other16.421
r_dihedral_angle_6_deg15.782
r_dihedral_angle_3_deg13.072
r_scbond_it11.042
r_scbond_other11.041
r_mcangle_it10.245
r_mcangle_other10.242
RMS Deviations
KeyRefinement Restraint Deviation
r_lrange_it19.605
r_lrange_other19.601
r_scangle_it16.426
r_scangle_other16.421
r_dihedral_angle_6_deg15.782
r_dihedral_angle_3_deg13.072
r_scbond_it11.042
r_scbond_other11.041
r_mcangle_it10.245
r_mcangle_other10.242
r_dihedral_angle_1_deg6.961
r_dihedral_angle_2_deg6.961
r_mcbond_it6.832
r_mcbond_other6.822
r_rigid_bond_restr4.03
r_angle_refined_deg1.668
r_angle_other_deg0.58
r_symmetry_nbd_refined0.3
r_nbd_refined0.215
r_nbd_other0.21
r_symmetry_nbd_other0.206
r_nbtor_refined0.181
r_xyhbond_nbd_refined0.127
r_chiral_restr0.085
r_symmetry_nbtor_other0.084
r_symmetry_xyhbond_nbd_refined0.058
r_dihedral_angle_other_2_deg0.057
r_bond_refined_d0.009
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 Atoms55
Heterogen Atoms32

Software

Software
Software NamePurpose
REFMACrefinement
Cootmodel building
MOLREPphasing
Aimlessdata scaling
XDSdata reduction