X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1AFKSingle RNase molecule from PDB-ID

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.5291PROTEIN WAS CRYSTALLIZED FROM 25% PEG 3350, 20 MM SODIUM CITRATE, PH 5.5, Glycinyl-5'-O-adenosine phosphoramidate soaking was achieved as follows. 1 uL of a stock solution of 50 mM ligand was added to 2uL of reservoir solution, to achieve a concentration of ~25 mM in the soaking solution. A few RNase A crystals were soaked for 45 - 90 minutes in the soaking solution
Crystal Properties
Matthews coefficientSolvent content
2.2445.03

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 101.002α = 90
b = 32.795β = 90.33
c = 74.09γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-300C(111)2019-07-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.97872APS21-ID-G

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.8829.8198.20.0940.09424.937.119587
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.881.9789.50.9510.9516.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTSingle RNase molecule from PDB-ID1.8829.811861896896.970.207690.204820.26463RANDOM43.318
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]
-1.83-1.67-2.123.96
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.043
r_dihedral_angle_3_deg15.044
r_long_range_B_refined8.58
r_long_range_B_other8.564
r_dihedral_angle_4_deg7.406
r_dihedral_angle_1_deg7.101
r_scangle_other5.345
r_mcangle_it4.937
r_mcangle_other4.937
r_scbond_it3.606
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1902
Nucleic Acid Atoms
Solvent Atoms98
Heterogen Atoms53

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing