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Crystal structure of the Interleukin-4 variant T13D
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 6.5 298 52% Ammonium sulfate, 0.1M Sodium citrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.13 60.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.528 α = 90 b = 90.528 β = 90 c = 45.907 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 CCD MARRESEARCH 2002-08-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.9178 SLS X06SA
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 1.65 10.6 97.1 0.092 17.6 6.7 23378 22700
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 1.65 1.74 98.1 0.172 5.2 6.4
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 1.65 9.98 22700 21555 1142 0.22222 0.22222 0.22093 0.2277 0.24709 0.2151 RANDOM 21.067
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] -0.01 -0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.683 r_scangle_it 5.063 r_scbond_it 3.133 r_mcangle_it 1.928 r_angle_refined_deg 1.695 r_mcbond_it 1.091 r_symmetry_hbond_refined 0.389 r_symmetry_vdw_refined 0.359 r_nbd_refined 0.26 r_xyhbond_nbd_refined 0.247
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.683 r_scangle_it 5.063 r_scbond_it 3.133 r_mcangle_it 1.928 r_angle_refined_deg 1.695 r_mcbond_it 1.091 r_symmetry_hbond_refined 0.389 r_symmetry_vdw_refined 0.359 r_nbd_refined 0.26 r_xyhbond_nbd_refined 0.247 r_chiral_restr 0.11 r_bond_refined_d 0.018 r_gen_planes_refined 0.007 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 1049 Nucleic Acid Atoms Solvent Atoms 123 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling CNS phasing