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Crystal structure of the 5'->3' exoribonuclease Xrn1, E178Q mutant in Complex with Manganese
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 277 0.1M Tris, 0.9M LiCl, 13.5% PEG 6000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.53 65.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.267 α = 109.92 b = 132.581 β = 105.81 c = 144.066 γ = 104
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 315r 2010-03-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1.075 NSLS X29A
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 2.9 30 96.6 156403 150992 -3 -3
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 2.9 3 97.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.92 30 149146 143344 7614 96.11 0.24942 0.24754 0.2843 0.279 RANDOM 79.977
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] 2.17 4.1 3.6 2.17 3.35 1.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.806 r_dihedral_angle_3_deg 22.009 r_dihedral_angle_4_deg 18.996 r_dihedral_angle_1_deg 7.141 r_scangle_it 4.201 r_scbond_it 2.533 r_mcangle_it 1.836 r_angle_refined_deg 1.753 r_rigid_bond_restr 1.282 r_mcbond_it 0.996
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.806 r_dihedral_angle_3_deg 22.009 r_dihedral_angle_4_deg 18.996 r_dihedral_angle_1_deg 7.141 r_scangle_it 4.201 r_scbond_it 2.533 r_mcangle_it 1.836 r_angle_refined_deg 1.753 r_rigid_bond_restr 1.282 r_mcbond_it 0.996 r_chiral_restr 0.111 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 34009 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 4
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling