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Structure of the mRNA-binding domain of elongation factor SelB from E.coli in complex with SECIS RNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1WSU PDB ENTRY 1WSU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 298 6.7 mM calcium chloride, 33 mM sodium acetate ,10% 2-methyl-2,4-pentanediol, 0.17M sodium fluoride (final), pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.26 62.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.498 α = 90 b = 56.515 β = 95.6 c = 48.414 γ = 90
Symmetry Space Group C 1 2 1
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 MAR CCD 165 mm mirrors 2005-11-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A 0.9797 ESRF BM30A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 51.503 95.7 0.101 0.101 5 3.5 17473 18032 38.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2 2.11 92.8 0.94 0.94 0.6 2.6 2545
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 1WSU 2.3 51.5 11957 850 95.59 0.204 0.2 0.1995 0.251 0.2511 RANDOM 31.599
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] -1.73 -0.01 0.47 1.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.278 r_dihedral_angle_4_deg 24.846 r_dihedral_angle_3_deg 21.834 r_dihedral_angle_1_deg 7.225 r_scangle_it 4.134 r_scbond_it 3.047 r_angle_refined_deg 2.463 r_mcangle_it 1.968 r_mcbond_it 1.057 r_metal_ion_refined 0.468
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.278 r_dihedral_angle_4_deg 24.846 r_dihedral_angle_3_deg 21.834 r_dihedral_angle_1_deg 7.225 r_scangle_it 4.134 r_scbond_it 3.047 r_angle_refined_deg 2.463 r_mcangle_it 1.968 r_mcbond_it 1.057 r_metal_ion_refined 0.468 r_symmetry_metal_ion_refined 0.46 r_nbtor_refined 0.304 r_symmetry_vdw_refined 0.292 r_xyhbond_nbd_refined 0.238 r_nbd_refined 0.237 r_chiral_restr 0.161 r_symmetry_hbond_refined 0.127 r_bond_refined_d 0.021 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 982 Nucleic Acid Atoms 491 Solvent Atoms 112 Heterogen Atoms 24
Software Software Software Name Purpose SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction Xnemo data collection MOSFLM data reduction