8OLJ

Crystal structure of Archaeoglobus fulgidus AfAgo-N protein representing N-L1-L2 domains


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 8OLD 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP280Protein concentration 4.1 mg/ml. Reservoir: TrisHCl pH 8.0 0.05 M; iPrOH 27%; ammonium acetate 0.11 M; Bicine pH 9.0 0.05 M. Cryo-protection: short wash in 0.16 M Ammonium acetate; 0.08 M TrisHCl pH 8.5; 24% iPrOH; Glycerol 20%
Crystal Properties
Matthews coefficientSolvent content
2.4750.12

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.264α = 90
b = 75.264β = 90
c = 94.722γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 X 6M2018-11-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)0.97970PETRA III, EMBL c/o DESYP13 (MX1)

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
11.494.721000.0470.0490.0160.99923.89.76162419.676
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.41.421000.9080.9670.3310.812.38.4

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 REPLACEMENTTHROUGHOUT1.453.755371620899.990.14790.144580.17772RANDOM25.532
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]
-0.04-0.02-0.040.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.358
r_dihedral_angle_4_deg12.05
r_dihedral_angle_3_deg11.859
r_dihedral_angle_1_deg6.352
r_long_range_B_refined6.031
r_rigid_bond_restr5.102
r_scbond_it4.848
r_mcangle_it2.997
r_mcbond_it2.313
r_angle_refined_deg1.61
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.358
r_dihedral_angle_4_deg12.05
r_dihedral_angle_3_deg11.859
r_dihedral_angle_1_deg6.352
r_long_range_B_refined6.031
r_rigid_bond_restr5.102
r_scbond_it4.848
r_mcangle_it2.997
r_mcbond_it2.313
r_angle_refined_deg1.61
r_chiral_restr0.108
r_bond_refined_d0.01
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_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_other
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1926
Nucleic Acid Atoms
Solvent Atoms265
Heterogen Atoms81

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing