1VC5

Crystal Structure of the Wild Type Hepatitis Delta Virus Gemonic Ribozyme Precursor, in EDTA solution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6277EDTA, NaCl, MPD, Sodium Cacodylate, Spermine-HCl, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
3.4363.91

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 109.488α = 90
b = 109.488β = 90
c = 187.58γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray80CCDADSC QUANTUM 4graphite2003-03-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.11.0781ALS8.2.1

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
13.48093.76744632212
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
3.43.48681.5

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 REPLACEMENTTHROUGHOUT3.4206744563632296.960.310.306010.304860.32706RANDOM40.392
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]
-2.34-1.17-2.343.51
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it10.322
r_scbond_it7.12
r_mcangle_it6.31
r_mcbond_it3.632
r_dihedral_angle_1_deg2.815
r_angle_refined_deg0.937
r_symmetry_hbond_refined0.686
r_symmetry_vdw_refined0.469
r_nbd_refined0.129
r_xyhbond_nbd_refined0.101
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it10.322
r_scbond_it7.12
r_mcangle_it6.31
r_mcbond_it3.632
r_dihedral_angle_1_deg2.815
r_angle_refined_deg0.937
r_symmetry_hbond_refined0.686
r_symmetry_vdw_refined0.469
r_nbd_refined0.129
r_xyhbond_nbd_refined0.101
r_chiral_restr0.046
r_bond_refined_d0.006
r_gen_planes_refined0.001
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms759
Nucleic Acid Atoms1489
Solvent Atoms
Heterogen Atoms2

Software

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