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Crystal structure of human CCL5 trimer
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EQT 1EQT monomer
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 283 0.2M ammonium sulfate, 0.1M BIS-TRIS pH 5, 16% (w/v) polyethylene glycol 3350
Crystal Properties Matthews coefficient Solvent content 2.58 52.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.556 α = 90 b = 56.556 β = 90 c = 154.103 γ = 90
Symmetry Space Group P 41 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315 2016-08-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13B1 1 NSRRC BL13B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.63 53.09 94.9 0.067 48.73 7.2 30546
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 1.63 1.66 0.889
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1EQT monomer 1.63 53.09 28967 1504 94.84 0.2026 0.20127 0.22844 0.2371 RANDOM 38.535
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] -1.54 -1.54 3.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.256 r_dihedral_angle_4_deg 16.349 r_dihedral_angle_3_deg 15.829 r_long_range_B_refined 8.381 r_long_range_B_other 8.16 r_dihedral_angle_1_deg 7.486 r_scangle_other 4.678 r_scbond_it 3.588 r_mcangle_it 3.328 r_mcangle_other 3.327
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.256 r_dihedral_angle_4_deg 16.349 r_dihedral_angle_3_deg 15.829 r_long_range_B_refined 8.381 r_long_range_B_other 8.16 r_dihedral_angle_1_deg 7.486 r_scangle_other 4.678 r_scbond_it 3.588 r_mcangle_it 3.328 r_mcangle_other 3.327 r_scbond_other 3.097 r_angle_refined_deg 2.48 r_mcbond_it 2.324 r_mcbond_other 2.324 r_angle_other_deg 1.38 r_chiral_restr 0.159 r_bond_refined_d 0.028 r_gen_planes_refined 0.014 r_bond_other_d 0.006 r_gen_planes_other 0.002 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 1580 Nucleic Acid Atoms Solvent Atoms 194 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data scaling MOLREP phasing Coot model building