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Crystal structure of the interleukin-4 variant R85A
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 61.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.19 α = 90 b = 91.19 β = 90 c = 45.77 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 Mirror 2004-08-21 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 2.35 32.3 98.9 0.056 17.3 4.4 8464 8375
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 2.35 2.43 99.6 0.265 4.6 4.3
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 2.5 20 7065 6654 334 98.95 0.21352 0.21352 0.21091 0.2131 0.26368 0.27 RANDOM 34.463
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] 0.65 0.65 -1.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.613 r_scangle_it 3.598 r_scbond_it 2.065 r_angle_refined_deg 1.4 r_mcangle_it 1.367 r_mcbond_it 0.705 r_symmetry_vdw_refined 0.291 r_symmetry_hbond_refined 0.28 r_xyhbond_nbd_refined 0.259 r_nbd_refined 0.244
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.613 r_scangle_it 3.598 r_scbond_it 2.065 r_angle_refined_deg 1.4 r_mcangle_it 1.367 r_mcbond_it 0.705 r_symmetry_vdw_refined 0.291 r_symmetry_hbond_refined 0.28 r_xyhbond_nbd_refined 0.259 r_nbd_refined 0.244 r_chiral_restr 0.088 r_bond_refined_d 0.012 r_gen_planes_refined 0.004 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 1042 Nucleic Acid Atoms Solvent Atoms 104 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement CrystalClear data reduction CrystalClear data scaling CNS phasing