5VCF | pdb_00005vcf

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 DROP729550 mM MgCl2, 200 mM Lithium sulfate monohydrate, 100 mM 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 = 71.073α = 90
b = 71.073β = 90
c = 71.274γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray99CCDADSC QUANTUM 3152016-09-16MSINGLE 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)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
12.85099.70.0720.0580.983.33296
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)
12.82.91000.5120.4950.8861.533.3

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4FNJ2.846.58315414299.670.165170.163130.170.213350.21RANDOM64.45
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]
0.190.10.19-0.62
RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_other10.847
r_long_range_B_refined10.812
r_scangle_other8.716
r_scbond_other6.387
r_scbond_it6.386
r_angle_refined_deg1.89
r_angle_other_deg1.739
r_chiral_restr0.108
r_gen_planes_refined0.012
r_bond_refined_d0.009
RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_other10.847
r_long_range_B_refined10.812
r_scangle_other8.716
r_scbond_other6.387
r_scbond_it6.386
r_angle_refined_deg1.89
r_angle_other_deg1.739
r_chiral_restr0.108
r_gen_planes_refined0.012
r_bond_refined_d0.009
r_bond_other_d0.005
r_gen_planes_other0.003
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 Atoms719
Solvent Atoms
Heterogen Atoms29

Software

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