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Crystal structure of Archaeoglobus fulgidus AfAgo-N protein representing N-L1-L2 domains
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8OK9 After phasing of data 8OK9 with AfAgo protein (2BGG) AfAgo-N protein became partly visible
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 280 NaCl 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 coefficient Solvent content 2.29 46.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.033 α = 73.94 b = 57.843 β = 89.56 c = 61.622 γ = 89.75
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 X 6M 2016-12-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 0.97680 PETRA III, EMBL c/o DESY P14 (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) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.85 55.59 93.2 0.033 0.044 0.033 0.999 15.9 3.6 44415 31.841
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) Redundancy Number Unique Reflections (All) 1 1.85 1.95 93.5 0.696 0.492 0.817 3.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.85 47.63 39974 4433 93.23 0.18299 0.17916 0.21819 0.2163 RANDOM 37.501
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] 0.05 0.1 0.11 1.2 2.15 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.848 r_dihedral_angle_3_deg 14.974 r_dihedral_angle_4_deg 12.999 r_long_range_B_refined 8.899 r_dihedral_angle_1_deg 6.377 r_mcangle_it 4.76 r_scbond_it 4.716 r_mcbond_it 3.305 r_angle_refined_deg 1.527 r_chiral_restr 0.116
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.848 r_dihedral_angle_3_deg 14.974 r_dihedral_angle_4_deg 12.999 r_long_range_B_refined 8.899 r_dihedral_angle_1_deg 6.377 r_mcangle_it 4.76 r_scbond_it 4.716 r_mcbond_it 3.305 r_angle_refined_deg 1.527 r_chiral_restr 0.116 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 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 Atoms Number Protein Atoms 3717 Nucleic Acid Atoms Solvent Atoms 272 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing