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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 2.65 53.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.404 α = 86.7 b = 46.763 β = 73.76 c = 66.24 γ = 84.53
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 PILATUS3 6M 2023-06-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.97856 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 2.09 63.56 96.1 0.991 5.1 2.4 26547
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 2.09 2.2 0.861
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 2.09 63.56 25269 1277 96.11 0.214 0.21076 0.219 0.27864 0.2811 RANDOM 32.173
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] 0.41 1.03 -0.38 1.11 2.13 -1.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.262 r_dihedral_angle_4_deg 17.059 r_dihedral_angle_3_deg 16.204 r_dihedral_angle_1_deg 7.486 r_long_range_B_other 7.386 r_long_range_B_refined 7.38 r_scangle_other 5.247 r_mcangle_it 4.426 r_mcangle_other 4.425 r_scbond_it 3.416
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.262 r_dihedral_angle_4_deg 17.059 r_dihedral_angle_3_deg 16.204 r_dihedral_angle_1_deg 7.486 r_long_range_B_other 7.386 r_long_range_B_refined 7.38 r_scangle_other 5.247 r_mcangle_it 4.426 r_mcangle_other 4.425 r_scbond_it 3.416 r_scbond_other 3.4 r_mcbond_it 2.929 r_mcbond_other 2.928 r_angle_refined_deg 1.618 r_angle_other_deg 1.308 r_chiral_restr 0.078 r_bond_refined_d 0.01 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 3162 Nucleic Acid Atoms Solvent Atoms 86 Heterogen Atoms 64
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data reduction HKL-3000 data scaling PHASER phasing