5V9Z

RNA hairpin structure containing 2-MeImpG analogue bound


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.529150 mM MgCl2, 3 M ammonia sulfate, 100 mM HEPES 7.5
Crystal Properties
Matthews coefficientSolvent content
3.6466.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.275α = 90
b = 45.275β = 90
c = 154.573γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray99CCDADSC QUANTUM 3152016-01-26MSINGLE 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
12.55095.40.10.0890.97616.310.65769
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)
12.52.5973.10.710.4860.9121.77.2

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 REPLACEMENTTHROUGHOUT4fnj2.5143.45546630295.510.221610.218120.28106RANDOM73.171
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]
0.030.03-0.07
RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_refined9.754
r_long_range_B_other9.749
r_scangle_other8.982
r_scbond_it7.261
r_scbond_other7.257
r_angle_other_deg2.541
r_angle_refined_deg2.438
r_chiral_restr0.244
r_bond_other_d0.022
r_bond_refined_d0.013
RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_refined9.754
r_long_range_B_other9.749
r_scangle_other8.982
r_scbond_it7.261
r_scbond_other7.257
r_angle_other_deg2.541
r_angle_refined_deg2.438
r_chiral_restr0.244
r_bond_other_d0.022
r_bond_refined_d0.013
r_gen_planes_refined0.013
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 Atoms709
Solvent Atoms12
Heterogen Atoms29

Software

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