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Structural and Functional insights into the human Upf1 helicase core
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GJK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 7.5 295 100mM Tris, 8-13% PEG3350, 140mM (NH4)3PO4, 10% EG, 10mM DTT, pH 7.5, EVAPORATION, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.25 45.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.284 α = 114.41 b = 67.836 β = 90.13 c = 87.25 γ = 110.22
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 2.4 20 90.8 43423
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 2GJK 2.4 20 41163 2207 90.88 0.23709 0.2352 0.2394 0.27193 0.2531 RANDOM 32.418
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] -0.97 1.53 1.21 3.32 2.56 0.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.145 r_scangle_it 1.657 r_angle_refined_deg 1.126 r_scbond_it 0.944 r_mcangle_it 0.922 r_angle_other_deg 0.79 r_mcbond_it 0.487 r_symmetry_hbond_refined 0.243 r_symmetry_vdw_other 0.224 r_nbd_other 0.217
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.145 r_scangle_it 1.657 r_angle_refined_deg 1.126 r_scbond_it 0.944 r_mcangle_it 0.922 r_angle_other_deg 0.79 r_mcbond_it 0.487 r_symmetry_hbond_refined 0.243 r_symmetry_vdw_other 0.224 r_nbd_other 0.217 r_nbd_refined 0.184 r_xyhbond_nbd_refined 0.154 r_symmetry_vdw_refined 0.124 r_nbtor_other 0.085 r_chiral_restr 0.061 r_bond_other_d 0.011 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 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 9496 Nucleic Acid Atoms Solvent Atoms 233 Heterogen Atoms 66
Software Software Software Name Purpose REFMAC refinement ADSC data collection CCP4 data scaling AMoRE phasing