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hAGO2-MID in complex with a chemical modified uridine monophosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3LUJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 290 0.25M Ammonium sulfate
0.1M Sodium cacodylate trihydrate pH 6.5
30% w/v Polyethylene glycol 8,000
Crystal Properties Matthews coefficient Solvent content 2.71 54.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.693 α = 86.34 b = 47.311 β = 73.58 c = 66.431 γ = 84.07
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 2023-06-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.97853 SSRF BL18U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.05 47.07 96.3 0.998 11.2 3.3 28673
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.05 2.16 0.844
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.05 47.07 27280 1391 96.35 0.20737 0.20499 0.2109 0.25439 0.2544 RANDOM 39.48
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] -0.18 1.38 -0.11 2.97 0.14 -2.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.988 r_dihedral_angle_3_deg 16.296 r_dihedral_angle_4_deg 14.212 r_long_range_B_other 8.659 r_long_range_B_refined 8.648 r_dihedral_angle_1_deg 6.873 r_scangle_other 6.186 r_mcangle_it 4.822 r_mcangle_other 4.822 r_scbond_it 3.974
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.988 r_dihedral_angle_3_deg 16.296 r_dihedral_angle_4_deg 14.212 r_long_range_B_other 8.659 r_long_range_B_refined 8.648 r_dihedral_angle_1_deg 6.873 r_scangle_other 6.186 r_mcangle_it 4.822 r_mcangle_other 4.822 r_scbond_it 3.974 r_scbond_other 3.947 r_mcbond_it 3.351 r_mcbond_other 3.333 r_angle_refined_deg 1.987 r_angle_other_deg 1.74 r_chiral_restr 0.319 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3141 Nucleic Acid Atoms Solvent Atoms 108 Heterogen Atoms 101
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data reduction HKL-3000 data scaling PHASER phasing