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Crystal structure of the interleukin-4 variant T13DR85A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1HIK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 294 52% Ammonium sulfate, 0.1M Sodium citrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.9 61.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.33 α = 90 b = 91.33 β = 90 c = 45.78 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 93 IMAGE PLATE RIGAKU RAXIS IV Rigaku VariMax mirror 2004-08-19 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 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 2.1 45.7 99.4 0.055 18.2 5.2 11800 11729
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 2.1 2.18 98.7 0.258 5.6 5.2
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 1HIK 2.1 20 11780 11162 555 99.47 0.21609 0.21609 0.21445 0.2111 0.24874 0.2466 RANDOM 22.064
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] 0.63 0.63 -1.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.044 r_scangle_it 4.593 r_scbond_it 2.788 r_mcangle_it 1.715 r_angle_refined_deg 1.661 r_mcbond_it 0.87 r_symmetry_hbond_refined 0.362 r_symmetry_vdw_refined 0.344 r_xyhbond_nbd_refined 0.274 r_nbd_refined 0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.044 r_scangle_it 4.593 r_scbond_it 2.788 r_mcangle_it 1.715 r_angle_refined_deg 1.661 r_mcbond_it 0.87 r_symmetry_hbond_refined 0.362 r_symmetry_vdw_refined 0.344 r_xyhbond_nbd_refined 0.274 r_nbd_refined 0.24 r_chiral_restr 0.118 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_refined 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 1043 Nucleic Acid Atoms Solvent Atoms 104 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement CrystalClear data reduction CrystalClear data scaling CNS phasing