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Crystal structure of Aa-Ago with externally-bound siRNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YVU Aa-Ago, pdb entry 1YVU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 20% PEG 3350, 25mM NH4F , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.53 51.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.697 α = 90 b = 117.516 β = 99.12 c = 98.62 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARRESEARCH 2005-06-20 M SINGLE WAVELENGTH 2 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1.1 NSLS X29A 2 SYNCHROTRON NSLS BEAMLINE X12C 1.1 NSLS X12C
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 3 40 0.952 0.051 6.9 38034 1 1
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 3 3.1 0.913 0.304 6.7 3596
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 Aa-Ago, pdb entry 1YVU 3 40 2 32694 32694 1741 95.6 0.25 0.21717 0.21233 0.2096 0.30736 0.3013 RANDOM 73.627
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] 1.11 -3.1 1.23 -3.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.69 r_dihedral_angle_3_deg 22.977 r_dihedral_angle_4_deg 21.317 r_dihedral_angle_1_deg 7.782 r_scangle_it 2.524 r_angle_refined_deg 1.699 r_scbond_it 1.489 r_mcangle_it 1.323 r_mcbond_it 0.72 r_nbtor_refined 0.324
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.69 r_dihedral_angle_3_deg 22.977 r_dihedral_angle_4_deg 21.317 r_dihedral_angle_1_deg 7.782 r_scangle_it 2.524 r_angle_refined_deg 1.699 r_scbond_it 1.489 r_mcangle_it 1.323 r_mcbond_it 0.72 r_nbtor_refined 0.324 r_symmetry_vdw_refined 0.276 r_nbd_refined 0.257 r_symmetry_hbond_refined 0.247 r_xyhbond_nbd_refined 0.177 r_chiral_restr 0.102 r_bond_refined_d 0.015 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11728 Nucleic Acid Atoms 930 Solvent Atoms 30 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MLPHARE phasing