5VCI

RNA hairpin structure containing tetraloop/receptor motif, complexed with 2-MeImpG analogue


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP729150 mM MgCl2, 0.2 M Lithium sulfate monohydrate, 0.1 M BIS-TRIS pH 7.0, 25% w/v Polyethylene glycol 3,350
Crystal Properties
Matthews coefficientSolvent content
3.261.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 69.612α = 90
b = 69.612β = 90
c = 70.853γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray99CCDADSC QUANTUM 3152016-10-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.21ALS8.2.2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (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
12.65097.80.0540.0520.94418.453.23864
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.62.6987.80.5260.810.5231.812.4

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 REPLACEMENTTHROUGHOUT4FNJ2.645.91364921597.80.164870.16230.21232RANDOM75.432
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]
-0.17-0.09-0.170.56
RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_other11.027
r_long_range_B_refined10.992
r_scangle_other9.512
r_scbond_it6.77
r_scbond_other6.77
r_angle_refined_deg1.787
r_angle_other_deg1.732
r_chiral_restr0.095
r_gen_planes_refined0.012
r_bond_refined_d0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_other11.027
r_long_range_B_refined10.992
r_scangle_other9.512
r_scbond_it6.77
r_scbond_other6.77
r_angle_refined_deg1.787
r_angle_other_deg1.732
r_chiral_restr0.095
r_gen_planes_refined0.012
r_bond_refined_d0.01
r_bond_other_d0.005
r_gen_planes_other0.002
r_dihedral_angle_1_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
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_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms
Nucleic Acid Atoms723
Solvent Atoms1
Heterogen Atoms29

Software

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