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Crystal structure of chicken cytokine interleukin 1 beta
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9ILB PDB ENTRY 9ILB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 10 PH 10
Crystal Properties Matthews coefficient Solvent content 1.93 35.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.739 α = 90 b = 38.476 β = 90 c = 102.111 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 293 CCD MARRESEARCH 2008-09-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13B1 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 1.58 30 99.7 0.05 31.54 6.7 20047 1.5
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 1.58 1.64 98.9 0.56 3.56 6.6
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 9ILB 1.58 30 18959 1015 99.6 0.189 0.187 0.1859 0.225 0.2223 RANDOM 20.66
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] 0.05 0.21 -0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.272 r_dihedral_angle_4_deg 18.467 r_dihedral_angle_3_deg 14.077 r_dihedral_angle_1_deg 7.583 r_sphericity_free 7.568 r_sphericity_bonded 5.686 r_scangle_it 4.988 r_scbond_it 3.513 r_mcangle_it 2.772 r_rigid_bond_restr 2.583
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.272 r_dihedral_angle_4_deg 18.467 r_dihedral_angle_3_deg 14.077 r_dihedral_angle_1_deg 7.583 r_sphericity_free 7.568 r_sphericity_bonded 5.686 r_scangle_it 4.988 r_scbond_it 3.513 r_mcangle_it 2.772 r_rigid_bond_restr 2.583 r_mcbond_it 1.914 r_angle_refined_deg 1.536 r_nbtor_refined 0.31 r_symmetry_vdw_refined 0.229 r_nbd_refined 0.219 r_xyhbond_nbd_refined 0.127 r_chiral_restr 0.105 r_symmetry_hbond_refined 0.105 r_bond_refined_d 0.013 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1207 Nucleic Acid Atoms Solvent Atoms 72 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling CCP4I phasing