9LU0 | pdb_00009lu0

Crystal Structure of 5'-Deoxy-5'-methylthioadenosine phosphorylase from Aeropyrum pernix 333K


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
2.2806308346.1010628

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.049α = 90
b = 79.049β = 90
c = 233.166γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray333PIXELDECTRIS 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
11.5544.381000.0710.0790.035123.41041175
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)
1.551.581001.041.1580.5050.6632.610.2

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-VALUE1WTA1.5544.3841173203199.9730.1460.1450.15720.16730.180823.554
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]
0.0470.0240.047-0.154
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg15.569
r_dihedral_angle_3_deg13.197
r_lrange_it8.626
r_lrange_other8.624
r_dihedral_angle_2_deg7.721
r_scangle_it7.145
r_scangle_other7.143
r_dihedral_angle_1_deg6.839
r_scbond_it4.63
r_scbond_other4.629
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg15.569
r_dihedral_angle_3_deg13.197
r_lrange_it8.626
r_lrange_other8.624
r_dihedral_angle_2_deg7.721
r_scangle_it7.145
r_scangle_other7.143
r_dihedral_angle_1_deg6.839
r_scbond_it4.63
r_scbond_other4.629
r_mcangle_it3.465
r_mcangle_other3.464
r_mcbond_it2.342
r_mcbond_other2.34
r_angle_refined_deg1.935
r_angle_other_deg0.651
r_nbd_refined0.227
r_symmetry_nbd_other0.202
r_nbd_other0.188
r_nbtor_refined0.182
r_symmetry_nbd_refined0.144
r_xyhbond_nbd_refined0.135
r_chiral_restr0.098
r_symmetry_nbtor_other0.086
r_symmetry_xyhbond_nbd_refined0.075
r_dihedral_angle_other_2_deg0.024
r_bond_refined_d0.011
r_gen_planes_refined0.01
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 Atoms56
Heterogen Atoms22

Software

Software
Software NamePurpose
REFMACrefinement
Cootmodel building
MOLREPphasing
Aimlessdata scaling
XDSdata reduction