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Crystal structure of a heptameric ring complex of yeast SmF in spacegroup P4122
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1I81 PDB entry 1I81 truncated to poly-serine
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 289 PEG 3350, sodium acetate, pH 8.5, VAPOR DIFFUSION, SITTING DROP at 289K
Crystal Properties Matthews coefficient Solvent content 2.69 54.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.891 α = 90 b = 79.891 β = 90 c = 251.188 γ = 90
Symmetry Space Group P 41 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 AREA DETECTOR M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 0.9393 ESRF ID14-4
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 2.8 79 99.9 0.066 19.6 6.8 19819 84.2
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 2.8 2.95 0.39 4.6 7.1
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1I81 truncated to poly-serine 2.8 20 19819 19819 1075 99.96 0.25431 0.25431 0.25357 0.26783 0.2858 RANDOM 50.316
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] 0.48 0.48 -0.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 19.51 r_dihedral_angle_1_deg 4.618 r_scangle_it 4.532 r_scbond_it 2.641 r_mcangle_it 2.307 r_angle_refined_deg 2.096 r_mcbond_it 1.239 r_angle_other_deg 0.932 r_symmetry_hbond_refined 0.558 r_symmetry_vdw_refined 0.516
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 19.51 r_dihedral_angle_1_deg 4.618 r_scangle_it 4.532 r_scbond_it 2.641 r_mcangle_it 2.307 r_angle_refined_deg 2.096 r_mcbond_it 1.239 r_angle_other_deg 0.932 r_symmetry_hbond_refined 0.558 r_symmetry_vdw_refined 0.516 r_symmetry_vdw_other 0.294 r_nbd_refined 0.282 r_nbd_other 0.272 r_xyhbond_nbd_refined 0.195 r_chiral_restr 0.113 r_xyhbond_nbd_other 0.047 r_bond_refined_d 0.023 r_gen_planes_refined 0.009 r_gen_planes_other 0.006 r_bond_other_d 0.001 r_nbtor_other r_symmetry_hbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3837 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling AMoRE phasing REFMAC refinement CCP4 data scaling