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The crystal structure of fission yeast mRNA decapping enzyme Dcp1-Dcp2 complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2A6T PDB entries 2A6T, 2QKL experimental model PDB 2QKL PDB entries 2A6T, 2QKL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 285 8% Ethylene Glycol, 100 mM HEPES pH 7.0, 11.6% MPD, 4.4% PEG 4000 and 10 mM ATP, VAPOR DIFFUSION, HANGING DROP, temperature 285K
Crystal Properties Matthews coefficient Solvent content 2.72 54.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.289 α = 90 b = 161.443 β = 97.49 c = 91.386 γ = 90
Symmetry Space Group P 1 21 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 ADSC QUANTUM 315 2006-07-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.9792 ESRF ID29
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 90.54 99.9 0.13 3.6 48289 48226 2 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 2.87 99.9 0.323 3.3 3.6
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 (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 entries 2A6T, 2QKL 2.8 20 48289 45695 2373 99.88 0.23611 0.23339 0.2292 0.28923 0.231 RANDOM 57.918
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] 5.02 0.82 0.84 -5.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.251 r_dihedral_angle_3_deg 18.753 r_dihedral_angle_4_deg 17.63 r_dihedral_angle_1_deg 5.59 r_scangle_it 1.694 r_angle_refined_deg 1.241 r_mcangle_it 1.131 r_scbond_it 1.048 r_mcbond_it 0.633 r_nbtor_refined 0.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.251 r_dihedral_angle_3_deg 18.753 r_dihedral_angle_4_deg 17.63 r_dihedral_angle_1_deg 5.59 r_scangle_it 1.694 r_angle_refined_deg 1.241 r_mcangle_it 1.131 r_scbond_it 1.048 r_mcbond_it 0.633 r_nbtor_refined 0.312 r_symmetry_vdw_refined 0.26 r_nbd_refined 0.225 r_symmetry_hbond_refined 0.213 r_xyhbond_nbd_refined 0.158 r_chiral_restr 0.09 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11704 Nucleic Acid Atoms Solvent Atoms 108 Heterogen Atoms 62
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction ADSC data collection MOSFLM data reduction SCALA data scaling PHASES phasing