9LWB | pdb_00009lwb

Crystal Structure of 5'-Deoxy-5'-methylthioadenosine phosphorylase from Aeropyrum pernix 293K


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
2.2772674646.0214539

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.97α = 90
b = 78.97β = 90
c = 233.288γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293PIXELDECTRIS EIGER X 16M2024-06-24MSINGLE 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
11.6244.381000.10.1120.0490.99916.79.936099
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)
1.621.651001.2181.360.5990.6972.210

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-VALUE1WTA1.6244.3836097187199.9720.1460.14490.15860.17110.181522.513
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]
-0.08-0.04-0.080.26
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg15.265
r_dihedral_angle_3_deg12.606
r_dihedral_angle_2_deg7.852
r_lrange_it7.565
r_lrange_other7.552
r_dihedral_angle_1_deg6.731
r_scangle_it6.506
r_scangle_other6.504
r_scbond_it4.177
r_scbond_other4.177
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg15.265
r_dihedral_angle_3_deg12.606
r_dihedral_angle_2_deg7.852
r_lrange_it7.565
r_lrange_other7.552
r_dihedral_angle_1_deg6.731
r_scangle_it6.506
r_scangle_other6.504
r_scbond_it4.177
r_scbond_other4.177
r_mcangle_it2.742
r_mcangle_other2.741
r_mcbond_it1.932
r_mcbond_other1.93
r_angle_refined_deg1.831
r_angle_other_deg0.627
r_nbd_refined0.211
r_symmetry_nbd_other0.193
r_nbd_other0.181
r_nbtor_refined0.18
r_symmetry_nbd_refined0.156
r_xyhbond_nbd_refined0.132
r_symmetry_xyhbond_nbd_refined0.117
r_chiral_restr0.094
r_dihedral_angle_other_2_deg0.083
r_symmetry_nbtor_other0.083
r_bond_refined_d0.01
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 Atoms88
Heterogen Atoms22

Software

Software
Software NamePurpose
REFMACrefinement
Cootmodel building
MOLREPphasing
Aimlessdata scaling
XDSdata reduction