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Crystal structure of TLR7/Cpd-1 (SM-374527) complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5GMH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 PEG3350 or PEG8000, ammonium sulfate, sodium citrate pH 5.0, Tris-HCl pH 7.5, NaCl
Crystal Properties Matthews coefficient Solvent content 2.68 54.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.754 α = 90 b = 138.504 β = 90 c = 148.462 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 PILATUS3 S 2M 2016-11-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0000 Photon Factory BL-5A
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 2.77 50.01 100 0.994 27.4 13 52528
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 2.77 2.86 0.959
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 5GMH 2.77 50.01 49888 2550 99.9 0.2139 0.212 0.2158 0.2518 0.2552 RANDOM 34.391
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] -0.82 -0.46 1.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.768 r_dihedral_angle_4_deg 19.128 r_dihedral_angle_3_deg 16.504 r_dihedral_angle_1_deg 7.122 r_angle_refined_deg 1.684 r_angle_other_deg 1.102 r_chiral_restr 0.086 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_bond_other_d 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.768 r_dihedral_angle_4_deg 19.128 r_dihedral_angle_3_deg 16.504 r_dihedral_angle_1_deg 7.122 r_angle_refined_deg 1.684 r_angle_other_deg 1.102 r_chiral_restr 0.086 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_bond_other_d 0.004 r_gen_planes_other 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12470 Nucleic Acid Atoms Solvent Atoms 46 Heterogen Atoms 258
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling MOLREP phasing