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Determination of Solvent Content in Cavities in Interleukin-1 Using Experimentally-Phased Electron Density
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5I1B PDB ENTRY 5I1B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 298 Well solution of 2.2 - 2.8 M ammonium sulfate, 100 mM Tris, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K, pH 7.50
Crystal Properties Matthews coefficient Solvent content 3.22 61.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.506 α = 90 b = 54.506 β = 90 c = 75.359 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 4 1999-07-10 M SINGLE WAVELENGTH 2 1 3 1 4 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 SSRL BL9-2
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 1.5 27.2 99.9 0.04 64 9.1 35259 19.5
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) 1.5 1.55 100 0.298 8.1
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT NONE PDB ENTRY 5I1B 1.53 27.2 35287 35225 100 0.211 0.211 0.2054
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]
RMS Deviations Key Refinement Restraint Deviation t_dihedral_angle_d 18.684 t_it 14.285 t_angle_deg 2.946 t_nbd 0.039 t_bond_d 0.025 t_gen_planes 0.021 t_trig_c_planes 0.012 t_incorr_chiral_ct t_pseud_angle
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1224 Nucleic Acid Atoms Solvent Atoms 149 Heterogen Atoms 10
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling SHARP phasing TNT refinement PDB_EXTRACT data extraction EPMR phasing