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Crystal structure of monkey TLR7 in complex with guanosine and polyU
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3W3J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 PEG 6000, calcium acetate, HEPES pH 7.0
Crystal Properties Matthews coefficient Solvent content 3.23 61.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.084 α = 93.83 b = 111.335 β = 94.34 c = 113.376 γ = 91.48
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 2M-F 2015-06-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NE3A 1.0 Photon Factory AR-NE3A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.5 50.01 97.6 0.112 8.9 3.5 153109
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 2.5 2.64 0.921
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 3W3J 2.5 50.01 153109 7968 97.58 0.20961 0.20785 0.2117 0.24324 0.244 RANDOM 51.838
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] 0.73 3.17 -0.8 -0.78 -0.56 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.721 r_dihedral_angle_4_deg 22.725 r_dihedral_angle_3_deg 16.634 r_long_range_B_other 9.254 r_long_range_B_refined 9.253 r_scangle_other 7.308 r_dihedral_angle_1_deg 6.79 r_mcangle_it 5.677 r_mcangle_other 5.677 r_scbond_it 4.652
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.721 r_dihedral_angle_4_deg 22.725 r_dihedral_angle_3_deg 16.634 r_long_range_B_other 9.254 r_long_range_B_refined 9.253 r_scangle_other 7.308 r_dihedral_angle_1_deg 6.79 r_mcangle_it 5.677 r_mcangle_other 5.677 r_scbond_it 4.652 r_scbond_other 4.652 r_mcbond_it 3.799 r_mcbond_other 3.799 r_angle_refined_deg 1.737 r_angle_other_deg 1.217 r_chiral_restr 0.093 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_bond_other_d 0.006 r_gen_planes_other 0.005 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 25192 Nucleic Acid Atoms 256 Solvent Atoms 157 Heterogen Atoms 504
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing