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Crystal structure of monkey TLR7 in complex with R848
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5GMF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 PEG 3350, ammonium sulfate, sodium citrate pH 5.2
Crystal Properties Matthews coefficient Solvent content 2.79 55.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.099 α = 90 b = 140.093 β = 90 c = 151.068 γ = 90
Symmetry Space Group P 21 21 21
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 2016-03-12 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 2.2 50.01 98.8 0.103 21.3 13.5 100054
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 2.2 2.24 0.937
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 5GMF 2.2 50.01 100054 5212 98.65 0.18669 0.18471 0.1919 0.22483 0.2335 RANDOM 42.593
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] -0.08 -0.95 1.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.738 r_dihedral_angle_4_deg 21.091 r_dihedral_angle_3_deg 15.079 r_long_range_B_refined 9.507 r_long_range_B_other 9.49 r_scangle_other 7.698 r_dihedral_angle_1_deg 6.778 r_scbond_it 5.458 r_scbond_other 5.3 r_mcangle_it 5.011
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.738 r_dihedral_angle_4_deg 21.091 r_dihedral_angle_3_deg 15.079 r_long_range_B_refined 9.507 r_long_range_B_other 9.49 r_scangle_other 7.698 r_dihedral_angle_1_deg 6.778 r_scbond_it 5.458 r_scbond_other 5.3 r_mcangle_it 5.011 r_mcangle_other 5.011 r_mcbond_it 3.644 r_mcbond_other 3.643 r_angle_refined_deg 1.857 r_angle_other_deg 1.234 r_chiral_restr 0.105 r_bond_refined_d 0.017 r_gen_planes_refined 0.01 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 12500 Nucleic Acid Atoms Solvent Atoms 653 Heterogen Atoms 438
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing