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Structural and functional insights into the human Upf1 helicase core
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 6 295 50mM MES, 0.5-3% PEG4000, 0.005mM MgSO4, 10mM DTT, pH 6.0, EVAPORATION, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.86 56.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 188.979 α = 90 b = 188.979 β = 90 c = 44.872 γ = 90
Symmetry Space Group P 43 21 2
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 2005-03-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.9793 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 2.6 20 98.9 24357 24065 1 1
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 2.6 20 24065 1288 98.8 0.24617 0.24487 0.2422 0.271 0.2562 RANDOM 38.966
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] 0.18 0.18 -0.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.21 r_scangle_it 1.471 r_mcangle_it 1.072 r_angle_refined_deg 1.048 r_scbond_it 0.789 r_angle_other_deg 0.749 r_mcbond_it 0.578 r_symmetry_vdw_refined 0.221 r_nbd_other 0.198 r_symmetry_vdw_other 0.188
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.21 r_scangle_it 1.471 r_mcangle_it 1.072 r_angle_refined_deg 1.048 r_scbond_it 0.789 r_angle_other_deg 0.749 r_mcbond_it 0.578 r_symmetry_vdw_refined 0.221 r_nbd_other 0.198 r_symmetry_vdw_other 0.188 r_nbd_refined 0.173 r_xyhbond_nbd_refined 0.122 r_symmetry_hbond_refined 0.089 r_nbtor_other 0.081 r_chiral_restr 0.056 r_bond_refined_d 0.006 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 4844 Nucleic Acid Atoms Solvent Atoms 110 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement ADSC data collection CCP4 data scaling SOLVE phasing