3DLB

Crystal structure of the guide-strand-containing Argonaute protein silencing complex


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.53085% PEGMME550, 0.1M KCl, 10mM MgCl2, 50 mM Tris HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 308K
Crystal Properties
Matthews coefficientSolvent content
2.5451.59

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.846α = 90
b = 123.399β = 95.7
c = 84.91γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2007-02-27MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-C0.97918, 0.97929APS24-ID-C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.7500.0629.44.542559
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)
2.72.81000.6431.724.6

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMADTHROUGHOUT2.7304384741328218897.630.25430.2931RANDOM54.033
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]
7.553-4.161-2.722-4.831
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.858
r_dihedral_angle_3_deg19.681
r_dihedral_angle_4_deg18.399
r_dihedral_angle_1_deg6.533
r_scangle_it2.581
r_angle_refined_deg1.874
r_scbond_it1.519
r_mcangle_it0.991
r_mcbond_it0.557
r_nbtor_refined0.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.858
r_dihedral_angle_3_deg19.681
r_dihedral_angle_4_deg18.399
r_dihedral_angle_1_deg6.533
r_scangle_it2.581
r_angle_refined_deg1.874
r_scbond_it1.519
r_mcangle_it0.991
r_mcbond_it0.557
r_nbtor_refined0.31
r_nbd_refined0.224
r_symmetry_vdw_refined0.215
r_symmetry_hbond_refined0.171
r_xyhbond_nbd_refined0.158
r_chiral_restr0.094
r_bond_refined_d0.012
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
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 Atoms9561
Nucleic Acid Atoms186
Solvent Atoms48
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing