☰ Navigation Tabs
Crystal structure of the complex between human nonsense mediated decay factors UPF1 and UPF2 Orthorhombic form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GK7 PDB ENTRIES 2GK7, 2IYK experimental model PDB 2IYK PDB ENTRIES 2GK7, 2IYK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6 1.6M AMMONIUM SULPHATE, 100 MM MES PH 6, 10% DIOXANE
Crystal Properties Matthews coefficient Solvent content 3.23 62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.91 α = 90 b = 129.14 β = 90 c = 311.27 γ = 90
Symmetry Space Group I 2 2 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 ADSC CCD 2008-03-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 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 2.5 30 98.4 0.11 11.2 3.71 45136
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 2.5 2.6 98 0.77 1.9 3.78
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 PDB ENTRIES 2GK7, 2IYK 2.5 46.52 42869 2266 98.38 0.19777 0.19552 0.2024 0.2403 0.2461 RANDOM 45.9
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] -0.72 0.35 0.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.747 r_dihedral_angle_4_deg 19.173 r_dihedral_angle_3_deg 17.786 r_dihedral_angle_1_deg 6.408 r_scangle_it 3.083 r_scbond_it 1.827 r_angle_refined_deg 1.386 r_mcangle_it 1.139 r_mcbond_it 0.575 r_chiral_restr 0.093
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.747 r_dihedral_angle_4_deg 19.173 r_dihedral_angle_3_deg 17.786 r_dihedral_angle_1_deg 6.408 r_scangle_it 3.083 r_scbond_it 1.827 r_angle_refined_deg 1.386 r_mcangle_it 1.139 r_mcbond_it 0.575 r_chiral_restr 0.093 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6107 Nucleic Acid Atoms Solvent Atoms 254 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing