8UB2 | pdb_00008ub2

Structure of Adenosine monophosphate/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. 5'-O-adenosine monophoshate 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 ~33 mM in the soaking solution. A few RNase A crystals were soaked for 160 - 180 minutes in the soaking solution
Crystal Properties
Matthews coefficientSolvent content
2.2445.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 101.054α = 90
b = 32.514β = 90.81
c = 72.935γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELBruker PHOTON II2023-09-05MSINGLE 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
11.620.6491.90.08355.472.2529170
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)
11.61.792.60.5421.351.35

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 REPLACEMENTTHROUGHOUT1.620.6427760137191.750.238030.236820.24430.262380.2707RANDOM22.54
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]
-0.590.6-0.010.58
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg14.235
r_dihedral_angle_1_deg7.268
r_dihedral_angle_2_deg6.645
r_long_range_B_refined6.3
r_long_range_B_other6.299
r_scangle_other4.45
r_mcangle_it3.515
r_mcangle_other3.514
r_scbond_it2.877
r_scbond_other2.876
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg14.235
r_dihedral_angle_1_deg7.268
r_dihedral_angle_2_deg6.645
r_long_range_B_refined6.3
r_long_range_B_other6.299
r_scangle_other4.45
r_mcangle_it3.515
r_mcangle_other3.514
r_scbond_it2.877
r_scbond_other2.876
r_mcbond_it2.357
r_mcbond_other2.357
r_angle_refined_deg1.489
r_angle_other_deg0.492
r_chiral_restr0.072
r_gen_planes_refined0.009
r_bond_refined_d0.008
r_bond_other_d0.001
r_gen_planes_other0.001
r_dihedral_angle_4_deg
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 Atoms1864
Nucleic Acid Atoms
Solvent Atoms104
Heterogen Atoms43

Software

Software
Software NamePurpose
REFMACrefinement
APEXdata reduction
APEXdata scaling
MOLREPphasing