3AO9

Crystal structure of the C-terminal domain of sequence-specific ribonuclease


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2DJH 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.527850mM MES, 0.1M cadmium chloride, 25% PEG MME, 15% glycerol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 278K
Crystal Properties
Matthews coefficientSolvent content
2.2244.57

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.71α = 90
b = 62.71β = 90
c = 100.51γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102006-11-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NW12A1.0000Photon FactoryAR-NW12A

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
12.15098.61391813723
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.1899.1

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 REPLACEMENTTHROUGHOUT2DJH2.147.78131881300668598.620.223590.221810.25866RANDOM32.563
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]
1.020.511.02-1.53
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.87
r_dihedral_angle_3_deg17.187
r_dihedral_angle_4_deg14.407
r_dihedral_angle_1_deg6.42
r_scangle_it4.944
r_scbond_it3.108
r_mcangle_it2.295
r_angle_refined_deg1.957
r_mcbond_it1.295
r_chiral_restr0.195
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.87
r_dihedral_angle_3_deg17.187
r_dihedral_angle_4_deg14.407
r_dihedral_angle_1_deg6.42
r_scangle_it4.944
r_scbond_it3.108
r_mcangle_it2.295
r_angle_refined_deg1.957
r_mcbond_it1.295
r_chiral_restr0.195
r_bond_refined_d0.022
r_gen_planes_refined0.009
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 Atoms1429
Nucleic Acid Atoms
Solvent Atoms114
Heterogen Atoms4

Software

Software
Software NamePurpose
ADSCdata collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling