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Crystal structure of human ERI1 exoribonuclease 3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1W0H PDB ENTRY 1W0H
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 0.1M TRIS PH 8.5 20% PEG MONOMETHYL ETHER 2000 0.2M TRIMETHYLAMINE N-OXIDE
Crystal Properties Matthews coefficient Solvent content 2.23 44.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.72 α = 90 b = 76.9 β = 90 c = 86.98 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 QUANTUM 315 2009-12-17 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 2.15 43.5 99.9 0.11 22.1 12.6 12879 2 24.2
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 2.15 2.3 100 0.48 6.3 13.5
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 ENTRY 1W0H 2.15 43.49 12235 644 100 0.17674 0.17497 0.1825 0.21014 0.2144 RANDOM 18.89
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] -0.01 1.03 -1.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.278 r_dihedral_angle_4_deg 17.91 r_dihedral_angle_3_deg 12.23 r_dihedral_angle_1_deg 6.743 r_scangle_it 2.047 r_scbond_it 1.609 r_angle_refined_deg 1.183 r_angle_other_deg 0.858 r_mcangle_it 0.851 r_mcbond_it 0.743
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.278 r_dihedral_angle_4_deg 17.91 r_dihedral_angle_3_deg 12.23 r_dihedral_angle_1_deg 6.743 r_scangle_it 2.047 r_scbond_it 1.609 r_angle_refined_deg 1.183 r_angle_other_deg 0.858 r_mcangle_it 0.851 r_mcbond_it 0.743 r_symmetry_vdw_other 0.286 r_nbd_refined 0.204 r_nbtor_refined 0.18 r_nbd_other 0.171 r_xyhbond_nbd_refined 0.163 r_symmetry_vdw_refined 0.15 r_symmetry_hbond_refined 0.132 r_mcbond_other 0.125 r_nbtor_other 0.084 r_chiral_restr 0.069 r_metal_ion_refined 0.051 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_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 1665 Nucleic Acid Atoms Solvent Atoms 104 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing