8UAZ | pdb_00008uaz

Structure of Glutamyl-5'-O-adenosine phosphoramidate/RNase A


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.5291PROTEIN WAS CRYSTALLIZED FROM 25 percent PEG 3350, 20 MM SODIUM CITRATE, PH 5.5. Glutaminyl-5'-O-adenosine phosphoramidate soaking was achieved as follows. 1 uL of a stock solution of 100 mM ligand was added to 2uL of reservoir solution, to achieve a concentration of ~35 mM in the soaking solution. A few RNase A crystals were soaked for 110 - 130 minutes in the soaking solution.
Crystal Properties
Matthews coefficientSolvent content
2.2545.36

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 101.255α = 90
b = 32.957β = 90.43
c = 73.987γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELBruker PHOTON II2023-01-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1LIQUID ANODEBRUKER METALJET1.3418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.7619.9398.90.094922.182024382
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.761.8693.90.7012.597.08

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.7619.9322845116897.390.210660.208740.21810.249350.2546RANDOM31.693
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]
-0.7-0.36-0.321.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.027
r_long_range_B_refined8.806
r_long_range_B_other8.803
r_dihedral_angle_2_deg8.318
r_dihedral_angle_1_deg7.711
r_scangle_other7.367
r_mcangle_it5.512
r_mcangle_other5.492
r_scbond_it4.912
r_scbond_other4.91
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.027
r_long_range_B_refined8.806
r_long_range_B_other8.803
r_dihedral_angle_2_deg8.318
r_dihedral_angle_1_deg7.711
r_scangle_other7.367
r_mcangle_it5.512
r_mcangle_other5.492
r_scbond_it4.912
r_scbond_other4.91
r_mcbond_it3.961
r_mcbond_other3.961
r_angle_refined_deg1.193
r_angle_other_deg0.449
r_chiral_restr0.059
r_bond_refined_d0.007
r_gen_planes_refined0.007
r_bond_other_d0.003
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1893
Nucleic Acid Atoms
Solvent Atoms97
Heterogen Atoms68

Software

Software
Software NamePurpose
REFMACrefinement
PROTEUM PLUSdata reduction
PROTEUM PLUSdata scaling
MOLREPphasing