7SZU

Crystal structure of Pepper RNA aptamer in complex with HBC ligand and Fab BL3-6


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4KZD 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP62980.02 M Magnesium sulfate hydrate 0.002 M Cobalt(II) chloride hexahydrate 0.05 M Sodium cacodylate trihydrate pH 6.0 25% v/v (+/-)-2-Methyl-2,4-pentanediol, 0.0005 M Spermine
Crystal Properties
Matthews coefficientSolvent content
3.1661.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.609α = 90
b = 96.992β = 90
c = 148.255γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray80PIXELDECTRIS EIGER X 16M2021-04-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-C0.979180APS24-ID-C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
12.239148.25599.90.99917.96.84364662.32
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.242.3199.21.4490.5930.6051.16.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE4KZD2.2458.91.3443546199999.80.22130.21940.262669.89
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d14.3669
f_angle_d0.5815
f_chiral_restr0.0375
f_plane_restr0.0034
f_bond_d0.0025
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3303
Nucleic Acid Atoms1407
Solvent Atoms546
Heterogen Atoms58

Software

Software
Software NamePurpose
PHENIXrefinement
Cootmodel building
MOSFLMdata reduction
SCALEPACKdata scaling
PHASERphasing