9JD2

Crystal Structure of 5'-Deoxy-5'-methylthioadenosine phosphorylase from Aeropyrum pernix complex with 5'-Deoxy-5'-methylthioadenosine 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, 5 mM MTA
Crystal Properties
Matthews coefficientSolvent content
2.2846.172

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.048α = 90
b = 79.048β = 90
c = 233.48γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray353PIXELDECTRIS EIGER X 16M2024-06-02MSINGLE 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
11.6239.521000.1410.1570.0690.9999.89.936182
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)
1.621.651002.5452.8381.2460.3441.110

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-VALUE1WTA1.6238.94436182182099.9530.1250.12280.167628.651
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]
-0.31-0.155-0.311.005
RMS Deviations
KeyRefinement Restraint Deviation
r_lrange_it20.207
r_lrange_other20.203
r_scangle_it16.317
r_scangle_other16.312
r_dihedral_angle_6_deg15.216
r_dihedral_angle_3_deg12.925
r_scbond_it10.958
r_scbond_other10.957
r_mcangle_it10.841
r_mcangle_other10.838
RMS Deviations
KeyRefinement Restraint Deviation
r_lrange_it20.207
r_lrange_other20.203
r_scangle_it16.317
r_scangle_other16.312
r_dihedral_angle_6_deg15.216
r_dihedral_angle_3_deg12.925
r_scbond_it10.958
r_scbond_other10.957
r_mcangle_it10.841
r_mcangle_other10.838
r_dihedral_angle_2_deg8.261
r_mcbond_it7.218
r_mcbond_other7.217
r_dihedral_angle_1_deg6.903
r_rigid_bond_restr4.187
r_angle_refined_deg1.688
r_angle_other_deg0.591
r_symmetry_nbd_refined0.233
r_nbd_other0.218
r_nbd_refined0.217
r_symmetry_nbd_other0.201
r_nbtor_refined0.18
r_symmetry_xyhbond_nbd_refined0.175
r_xyhbond_nbd_refined0.134
r_chiral_restr0.087
r_symmetry_nbtor_other0.083
r_dihedral_angle_other_2_deg0.018
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 Atoms47
Heterogen Atoms25

Software

Software
Software NamePurpose
REFMACrefinement
Cootmodel building
MOLREPphasing
Aimlessdata scaling
XDSdata reduction