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Crystal structure of murine interleukin-5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1HUL PDB ENTRY 1HUL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 294 26% PEG 4000, 0.1M Tris-HCl pH 8.5, 0.2M sodium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 1.93 36.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.193 α = 90 b = 47.085 β = 96.41 c = 55.053 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV++ VariMax Cu High-Res Multilayer 2006-08-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.5418
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 54.7 96.8 0.086 13.7 6.35 6951 6732 36
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.5 2.59 94.6 0.398 3.9 6.52 660
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 PDB ENTRY 1HUL 2.5 15.09 6951 6311 345 94.6 0.21483 0.21483 0.21346 0.2475 0.2401 0.2753 RANDOM 27.497
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] 0.16 -0.14 -0.05 -0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.052 r_dihedral_angle_4_deg 24.764 r_dihedral_angle_3_deg 24.55 r_dihedral_angle_1_deg 7.718 r_mcangle_it 2.154 r_scangle_it 1.961 r_angle_refined_deg 1.915 r_mcbond_it 1.278 r_scbond_it 1.248 r_symmetry_vdw_refined 0.338
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.052 r_dihedral_angle_4_deg 24.764 r_dihedral_angle_3_deg 24.55 r_dihedral_angle_1_deg 7.718 r_mcangle_it 2.154 r_scangle_it 1.961 r_angle_refined_deg 1.915 r_mcbond_it 1.278 r_scbond_it 1.248 r_symmetry_vdw_refined 0.338 r_nbtor_refined 0.329 r_xyhbond_nbd_refined 0.296 r_symmetry_hbond_refined 0.29 r_nbd_refined 0.286 r_chiral_restr 0.126 r_bond_refined_d 0.018 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1721 Nucleic Acid Atoms Solvent Atoms 74 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection CrystalClear data reduction CrystalClear data scaling PHASER phasing