1VGJ

Crystal structure of 2'-5' RNA ligase from Pyrococcus horikoshii


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1IUHPDB entry 1iuh

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.6293Ammonium acetate, Sodium acetate, PEG4000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.1943.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.5α = 90
b = 45.7β = 90
c = 97.6γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC2004-03-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL44B20.97950SPring-8BL44B2

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
11.945099.90.0470.04716.571433014330-350.2
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.942.0199.60.3840.3846.61394

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 1iuh1.9410141941278014141000.215840.210470.26487RANDOM33.802
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]
1.29-0.99-0.3
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it7.231
r_dihedral_angle_1_deg5.898
r_scbond_it4.291
r_mcangle_it2.848
r_angle_refined_deg1.966
r_mcbond_it1.602
r_symmetry_vdw_refined0.245
r_nbd_refined0.237
r_xyhbond_nbd_refined0.212
r_chiral_restr0.156
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it7.231
r_dihedral_angle_1_deg5.898
r_scbond_it4.291
r_mcangle_it2.848
r_angle_refined_deg1.966
r_mcbond_it1.602
r_symmetry_vdw_refined0.245
r_nbd_refined0.237
r_xyhbond_nbd_refined0.212
r_chiral_restr0.156
r_symmetry_hbond_refined0.143
r_bond_refined_d0.027
r_gen_planes_refined0.01
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1488
Nucleic Acid Atoms
Solvent Atoms41
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing