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Structure of the RNA recognition motif (RRM) of Seb1 from S. pombe., solved at wavelength 2.75 A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 1 M ammonium formate, 100 mM sodium cacodylate, 8% (w/v) poly-gamma-glutamic acid polymer (PGA-LM, 200-400 kDa low molecular weight polymer)
Crystal Properties Matthews coefficient Solvent content 2.39 48.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.1 α = 90 b = 46.9 β = 99 c = 32.3 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 80 PIXEL DECTRIS PILATUS 12M 2016-07-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I23 2.7552 Diamond I23
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.775 54.87 64.89 0.04513 0.04915 0.01897 0.999 22.91 6.1 10445 23.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.775 1.838 0.2519 0.919 3.26
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 1.77 54.87 9850 545 64.94 0.15652 0.15472 0.1632 0.18829 0.1876 RANDOM 22.71
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] -0.86 0.61 1.63 -0.92
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 24.522 r_dihedral_angle_4_deg 16.075 r_dihedral_angle_3_deg 11.9 r_dihedral_angle_1_deg 8.028 r_long_range_B_refined 5.637 r_long_range_B_other 5.598 r_scangle_other 4.667 r_scbond_it 3.308 r_scbond_other 3.258 r_mcangle_it 3.254
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 24.522 r_dihedral_angle_4_deg 16.075 r_dihedral_angle_3_deg 11.9 r_dihedral_angle_1_deg 8.028 r_long_range_B_refined 5.637 r_long_range_B_other 5.598 r_scangle_other 4.667 r_scbond_it 3.308 r_scbond_other 3.258 r_mcangle_it 3.254 r_mcangle_other 3.252 r_mcbond_it 2.435 r_mcbond_other 2.416 r_angle_refined_deg 1.094 r_angle_other_deg 1.086 r_chiral_restr 0.062 r_gen_planes_refined 0.026 r_gen_planes_other 0.017 r_bond_refined_d 0.01 r_bond_other_d 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1192 Nucleic Acid Atoms Solvent Atoms 85 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling HKL2Map phasing