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Crystal structure of S.pombe mRNA decapping enzyme Dcp2p
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.2 293 Na/K phosphate, PEG200, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.3 46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.481 α = 90 b = 56.481 β = 90 c = 301.528 γ = 120
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 210 2004-10-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.9798 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.5 20 18700 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.56
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 2.5 15 1 18635 17682 953 99.92 0.2549 0.24981 0.2476 0.2472 0.28878 0.2835 RANDOM 22.666
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] 2.8 1.4 2.8 -4.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.408 r_scangle_it 2.019 r_angle_refined_deg 1.317 r_scbond_it 1.233 r_mcangle_it 0.867 r_angle_other_deg 0.851 r_mcbond_it 0.464 r_nbd_other 0.222 r_nbd_refined 0.217 r_xyhbond_nbd_refined 0.212
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.408 r_scangle_it 2.019 r_angle_refined_deg 1.317 r_scbond_it 1.233 r_mcangle_it 0.867 r_angle_other_deg 0.851 r_mcbond_it 0.464 r_nbd_other 0.222 r_nbd_refined 0.217 r_xyhbond_nbd_refined 0.212 r_symmetry_hbond_refined 0.206 r_symmetry_vdw_other 0.203 r_symmetry_vdw_refined 0.15 r_nbtor_other 0.085 r_chiral_restr 0.079 r_bond_refined_d 0.012 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_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 3334 Nucleic Acid Atoms Solvent Atoms 107 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling SHARP phasing