☰ Navigation Tabs
Crystal structure of homomeric yeast Lsm3 exhibiting novel octameric ring organisation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1I81 PDB ENTRY 1I81
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 1.75M lithium sulfate, 8% (v/v) 2-methyl-2,4-pentanediol, 0.1M imidazole (pH 7.0), 10mM uridine-5-monophosphate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.83 56.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.743 α = 90 b = 83.743 β = 90 c = 141.931 γ = 90
Symmetry Space Group I 4 2 2
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 MARMOSAIC 300 mm CCD 2005-11-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 0.9793 APS 23-ID-D
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 2.45 36.25 97.6 0.086 23.7 9583 9073 2 2 71.8
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 2.45 2.57 83.9 1.405 1.5
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 PDB ENTRY 1I81 2.5 24.04 9073 8603 429 99.55 0.21694 0.21694 0.21564 0.2144 0.24296 0.2399 RANDOM 74.78
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 r_dihedral_angle_2_deg 34.878 r_dihedral_angle_3_deg 20.438 r_dihedral_angle_4_deg 17.688 r_dihedral_angle_1_deg 7.503 r_scangle_it 3.416 r_scbond_it 2.276 r_angle_refined_deg 2.125 r_mcangle_it 1.392 r_mcbond_it 0.798 r_nbtor_refined 0.324
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.878 r_dihedral_angle_3_deg 20.438 r_dihedral_angle_4_deg 17.688 r_dihedral_angle_1_deg 7.503 r_scangle_it 3.416 r_scbond_it 2.276 r_angle_refined_deg 2.125 r_mcangle_it 1.392 r_mcbond_it 0.798 r_nbtor_refined 0.324 r_symmetry_vdw_refined 0.308 r_nbd_refined 0.254 r_symmetry_hbond_refined 0.221 r_chiral_restr 0.129 r_xyhbond_nbd_refined 0.127 r_bond_refined_d 0.021 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1368 Nucleic Acid Atoms Solvent Atoms 2 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement MAR345dtb data collection MOSFLM data reduction SCALA data scaling PHASER phasing