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Crystal structure of Ago2 MID domain in complex with 6-(3-(2-carboxyethyl)phenyl)purine riboside monophosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6L45
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 277.15 0.1M imidazole pH8.0, 0.2M NaCl, 0.46M NaH2PO4, 1.84M K2HPO4
Crystal Properties Matthews coefficient Solvent content 2.6 52.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.28 α = 107.06 b = 66.46 β = 95.63 c = 40.42 γ = 86.4
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 6M 2014-11-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 0.98 Photon Factory BL-17A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.7 38.51 99.8 0.191 0.215 0.982 5.44 4.429 51572 37.512
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.8 99.5 1.1 1.307 0.601 1.44 3.351
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 6L45 1.7 38.51 48783 2589 99.8 0.1962 0.1944 0.2013 0.2286 0.2301 RANDOM 42.944
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] 0.51 0.14 -0.49 -0.57 0.57 -0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.788 r_dihedral_angle_4_deg 15.285 r_dihedral_angle_3_deg 15.173 r_dihedral_angle_1_deg 6.716 r_angle_refined_deg 1.717 r_angle_other_deg 1.377 r_chiral_restr 0.087 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.788 r_dihedral_angle_4_deg 15.285 r_dihedral_angle_3_deg 15.173 r_dihedral_angle_1_deg 6.716 r_angle_refined_deg 1.717 r_angle_other_deg 1.377 r_chiral_restr 0.087 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3103 Nucleic Acid Atoms Solvent Atoms 283 Heterogen Atoms 109
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction