9LR4 | pdb_00009lr4

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


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
2.2817699946.1279678

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.044α = 90
b = 79.044β = 90
c = 233.312γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray343PIXELDECTRIS EIGER X 16M2024-11-24MSINGLE 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
11.744.41000.0950.1050.0460.99920.81031368
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)
11.71.731001.1791.2880.5720.6762.59.8

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-VALUE1WTA1.744.431367161199.9710.1470.14520.15720.18190.188627.831
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]
0.1410.070.141-0.456
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg15.221
r_dihedral_angle_3_deg13.949
r_lrange_other10.346
r_lrange_it10.343
r_scangle_it8.237
r_scangle_other8.234
r_dihedral_angle_1_deg7.342
r_dihedral_angle_2_deg6.727
r_scbond_it5.161
r_scbond_other5.161
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg15.221
r_dihedral_angle_3_deg13.949
r_lrange_other10.346
r_lrange_it10.343
r_scangle_it8.237
r_scangle_other8.234
r_dihedral_angle_1_deg7.342
r_dihedral_angle_2_deg6.727
r_scbond_it5.161
r_scbond_other5.161
r_mcangle_it4.065
r_mcangle_other4.064
r_mcbond_it2.784
r_mcbond_other2.784
r_angle_refined_deg1.831
r_angle_other_deg0.606
r_symmetry_nbd_refined0.309
r_nbd_other0.223
r_nbd_refined0.22
r_symmetry_nbd_other0.201
r_nbtor_refined0.18
r_xyhbond_nbd_refined0.143
r_chiral_restr0.09
r_symmetry_nbtor_other0.087
r_dihedral_angle_other_2_deg0.07
r_symmetry_xyhbond_nbd_refined0.061
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 Atoms45
Heterogen Atoms22

Software

Software
Software NamePurpose
REFMACrefinement
Cootmodel building
MOLREPphasing
Aimlessdata scaling
XDSdata reduction