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Structure of the Argonaute protein from Methanocaldcoccus janaschii in complex with guide DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5G5S PDB ENTRY 5G5S
Crystallization Crystal Properties Matthews coefficient Solvent content 2.66 0.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.95 α = 90 b = 117.95 β = 90 c = 134.59 γ = 90
Symmetry Space Group P 43 21 2
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 PILATUS 2015-07-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.85 44.4 1 0.12 7.8 5.4 22659 1 102.61
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.85 3 99 1.25 1.1 5.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 5G5S 2.85 49.11 22659 1146 99.41 0.2315 0.2287 0.2525 0.285 0.3143 RANDOM 96.09
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] -0.6747 -0.6747 1.3494
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 23.51 t_omega_torsion 2.88 t_angle_deg 1.28 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 23.51 t_omega_torsion 2.88 t_angle_deg 1.28 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5239 Nucleic Acid Atoms 138 Solvent Atoms Heterogen Atoms 36
Software Software Software Name Purpose BUSTER refinement DIALS data reduction Aimless data scaling PHASER phasing