6C8E

RNA-imidazolium-bridged intermediate complex, 4h soaking


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5DHC 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP729110% v/v (+/-)-2-Methyl-2,4-pentanediol, 0.040 M Sodium cacodylate trihydrate pH 7.0, 0.012 M Spermine tetrahydrochloride, 0.080 M Sodium chloride
Crystal Properties
Matthews coefficientSolvent content
2.9157.75

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.023α = 90
b = 49.023β = 90
c = 81.317γ = 120
Symmetry
Space GroupP 3 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray99CCDMAR CCD 130 mm2017-04-04MSINGLE 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)Rrim I (All)Rpim I (All)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
11.85097.70.0980.1030.0330.97920.610.110695
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.861000.7130.7520.2360.9842.959.9

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 REPLACEMENTTHROUGHOUT5DHC1.842.461012356597.410.268220.267090.2897RANDOM52.894
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]
1.231.23-2.46
RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_other9.457
r_long_range_B_refined9.453
r_scangle_other8.202
r_scbond_it6.606
r_scbond_other6.603
r_angle_other_deg4.224
r_angle_refined_deg3.25
r_chiral_restr0.192
r_bond_other_d0.058
r_bond_refined_d0.028
RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_other9.457
r_long_range_B_refined9.453
r_scangle_other8.202
r_scbond_it6.606
r_scbond_other6.603
r_angle_other_deg4.224
r_angle_refined_deg3.25
r_chiral_restr0.192
r_bond_other_d0.058
r_bond_refined_d0.028
r_gen_planes_refined0.018
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 Atoms598
Solvent Atoms4
Heterogen Atoms104

Software

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