3IVK

Crystal Structure of the Catalytic Core of an RNA Polymerase Ribozyme Complexed with an Antigen Binding Antibody Fragment


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16277Fab-RNA: 10 mM Tris pH 7.6, 20.1 mM MgCl2, 0.1 mM EDTA, 150 mM NaCl. Screen solution: 50 mM cacodylate pH 6.0, 20 mM NaCl, 1 mM CdCl2, 32% MPD. Cryo: Paratone-N, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
4.1370.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 207.499α = 90
b = 206.452β = 90
c = 135.926γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayCCDMARMOSAIC 300 mm CCD2009-04-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-DAPS21-ID-D

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
13.15098.20.1556.16.752330
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)
13.13.1579.60.5853.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT3.15052239264898.20.2080.2070.225RANDOM68.09
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]
0.79-0.47-0.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.653
r_dihedral_angle_3_deg14.239
r_dihedral_angle_4_deg13.073
r_dihedral_angle_1_deg4.76
r_angle_refined_deg1.323
r_scangle_it1.25
r_scbond_it0.716
r_mcangle_it0.41
r_mcbond_it0.191
r_chiral_restr0.058
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.653
r_dihedral_angle_3_deg14.239
r_dihedral_angle_4_deg13.073
r_dihedral_angle_1_deg4.76
r_angle_refined_deg1.323
r_scangle_it1.25
r_scbond_it0.716
r_mcangle_it0.41
r_mcbond_it0.191
r_chiral_restr0.058
r_bond_refined_d0.006
r_gen_planes_refined0.003
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6604
Nucleic Acid Atoms5470
Solvent Atoms104
Heterogen Atoms37

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling