4DWR

RNA ligase RtcB/Mn2+ complex


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52981.5 M (NH4)2SO4, 75 mM NaCl, and 0.1 M HEPES-NaOH pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
3.3463.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 114.081α = 90
b = 84.899β = 115.65
c = 124.2γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDAPEX II CCD2011-07-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-E0.97918APS24-ID-E

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.55509531015329405821
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.541.6162.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.4846.743101532940581565387.650.143650.143650.141830.17794RANDOM30.239
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]
-1.83-1.331.55-0.87
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.033
r_dihedral_angle_4_deg17.286
r_dihedral_angle_3_deg14.035
r_scangle_it8.775
r_scbond_it6.477
r_dihedral_angle_1_deg5.944
r_mcangle_it5.618
r_mcbond_it4.048
r_rigid_bond_restr2.193
r_angle_refined_deg1.316
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.033
r_dihedral_angle_4_deg17.286
r_dihedral_angle_3_deg14.035
r_scangle_it8.775
r_scbond_it6.477
r_dihedral_angle_1_deg5.944
r_mcangle_it5.618
r_mcbond_it4.048
r_rigid_bond_restr2.193
r_angle_refined_deg1.316
r_chiral_restr0.087
r_bond_refined_d0.01
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_other
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11340
Nucleic Acid Atoms
Solvent Atoms1654
Heterogen Atoms180

Software

Software
Software NamePurpose
HKL-2000data collection
AMoREphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling