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Crystal structure of S. pombe Dcp2:Dcp1:Edc1 mRNA decapping complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5J3Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 4.8 292 1.55 M sodium formate, 0.1 M sodium acetate (pH 4.8)
Crystal Properties Matthews coefficient Solvent content 1.9 35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.809 α = 90 b = 41.371 β = 114.04 c = 93.718 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 PIXEL DECTRIS PILATUS 6M-F DYNAMICALLY BENDABLE MIRRORS 2015-04-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.000 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.6 45.1 99.1 0.028 18.9 3.2 45926 31.59
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.68 96.4 0.653 1.6 3.2
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 5J3Y 1.6 23.43 45762 2288 99.42 0.1876 0.186 0.1892 0.2191 0.2235 RANDOM 40.78
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] -0.8139 1.6285 -0.0984 0.9123
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 16.35 t_omega_torsion 3.49 t_angle_deg 1.05 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 16.35 t_omega_torsion 3.49 t_angle_deg 1.05 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3239 Nucleic Acid Atoms Solvent Atoms 215 Heterogen Atoms 16
Software Software Software Name Purpose BUSTER refinement XDS data reduction Aimless data scaling PHASER phasing