5HBW

RNA primer-template complex with 2-methylimidazole-activated monomer analogue


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1DNS 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7292(+/-)-2-Methyl-2,4-pentanediol, Sodium cacodylate trihydrate, Spermine tetrahydrochloride, Sodium chloride, Potassium chloride, Magnesium chloride hexahydrate
Crystal Properties
Matthews coefficientSolvent content
2.6553.51

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 28.076α = 90
b = 39.747β = 90
c = 42.593γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2015-10-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.10.987ALS8.2.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.95099.70.05324.86.1403640360.050.05
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.91.97990.5073.35.9

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 REPLACEMENTTHROUGHOUT1DNS1.923.44384119599.560.218570.216960.25416RANDOM33.77
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]
0.010.03-0.05
RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_refined5.501
r_long_range_B_other5.496
r_scangle_other4.877
r_angle_other_deg4.588
r_scbond_it3.58
r_scbond_other3.575
r_angle_refined_deg3.485
r_chiral_restr0.166
r_bond_other_d0.038
r_bond_refined_d0.037
RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_refined5.501
r_long_range_B_other5.496
r_scangle_other4.877
r_angle_other_deg4.588
r_scbond_it3.58
r_scbond_other3.575
r_angle_refined_deg3.485
r_chiral_restr0.166
r_bond_other_d0.038
r_bond_refined_d0.037
r_gen_planes_refined0.02
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 Atoms298
Solvent Atoms3
Heterogen Atoms58

Software

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