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Crystal structure of Ago2 MID domain in complex with 8-Br-adenosin-5'-monophosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3LUD
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 2.61 52.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.17 α = 105.83 b = 65.77 β = 96.46 c = 40.79 γ = 87.56
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 ADSC QUANTUM 210 2011-12-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.000 Photon Factory AR-NW12A
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 2 31.31 94.6 0.107 0.151 0.107 0.989 4.2 2 29976
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) Redundancy Number Unique Reflections (All) 1 2 2.05 93.9 0.758 1.072 0.758 0.45 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 3lud 2 30 28480 1495 94.56 0.2067 0.2043 0.2109 0.247 0.252 RANDOM 29.892
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] 1.02 0.19 -2.07 -1.83 0.65 0.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.357 r_dihedral_angle_3_deg 17.139 r_dihedral_angle_4_deg 13.881 r_dihedral_angle_1_deg 7.709 r_angle_refined_deg 1.546 r_angle_other_deg 1.265 r_chiral_restr 0.07 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.357 r_dihedral_angle_3_deg 17.139 r_dihedral_angle_4_deg 13.881 r_dihedral_angle_1_deg 7.709 r_angle_refined_deg 1.546 r_angle_other_deg 1.265 r_chiral_restr 0.07 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3119 Nucleic Acid Atoms Solvent Atoms 210 Heterogen Atoms 72
Software Software Software Name Purpose MOSFLM data reduction Aimless data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction