X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 8OK9After phasing of data 8OK9 with AfAgo protein (2BGG) AfAgo-N protein became partly visible

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6280NaCl 0.012 M; KCl 0.08 M; Sodium Cacodylate pH 6.0 0.04 M; MPD 50% ;spermin 0.012 M; 9 mg/ml protein concentration
Crystal Properties
Matthews coefficientSolvent content
2.2946.34

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.033α = 73.94
b = 57.843β = 89.56
c = 61.622γ = 89.75
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 X 6M2016-12-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)0.97680PETRA III, EMBL c/o DESYP14 (MX2)

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
11.8555.5993.20.0330.0440.0330.99915.93.64441531.841
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.851.9593.50.6960.4920.8173.6

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 REPLACEMENTFREE R-VALUE1.8547.6339974443393.230.182990.179160.21819RANDOM37.501
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]
0.050.10.111.22.15-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.848
r_dihedral_angle_3_deg14.974
r_dihedral_angle_4_deg12.999
r_long_range_B_refined8.899
r_dihedral_angle_1_deg6.377
r_mcangle_it4.76
r_scbond_it4.716
r_mcbond_it3.305
r_angle_refined_deg1.527
r_chiral_restr0.116
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.848
r_dihedral_angle_3_deg14.974
r_dihedral_angle_4_deg12.999
r_long_range_B_refined8.899
r_dihedral_angle_1_deg6.377
r_mcangle_it4.76
r_scbond_it4.716
r_mcbond_it3.305
r_angle_refined_deg1.527
r_chiral_restr0.116
r_bond_refined_d0.008
r_gen_planes_refined0.008
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_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3717
Nucleic Acid Atoms
Solvent Atoms272
Heterogen Atoms42

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing