1VBZ

Crystal Structure of the Hepatitis Delta Virus Gemonic Ribozyme Precursor, with C75U mutaion, in Ba2+ solution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6277BaCl2, NaCl, MPD, Sodium Cacodylate, Spermine-HCl, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
3.362.43

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 108.63α = 90
b = 108.63β = 90
c = 190.072γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray80CCDADSC QUANTUM 42003-02-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.3.11.1000ALS8.3.1

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
12.835.487.710911956922.839.2
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.82.9873.6

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 REPLACEMENTTHROUGHOUT2.833.4310911956956387.80.2550.2530.2530.268RANDOM68.4
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]
-6.74-0.1-6.7413.48
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d28.6
c_mcangle_it2.5
c_scangle_it2.34
c_scbond_it1.49
c_improper_angle_d1.44
c_mcbond_it1.26
c_angle_deg1.2
c_bond_d0.008
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d28.6
c_mcangle_it2.5
c_scangle_it2.34
c_scbond_it1.49
c_improper_angle_d1.44
c_mcbond_it1.26
c_angle_deg1.2
c_bond_d0.008
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms762
Nucleic Acid Atoms1552
Solvent Atoms20
Heterogen Atoms2

Software

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