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Structure of TREX1 in complex with a nucleotide and an inhibitor ion (lithium)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2O4G PDB ID 2o4g
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 22% PEG3350, 100 mM MES pH 6.0, 200 mM Li2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.25 45.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.619 α = 90 b = 81.337 β = 103.07 c = 92.706 γ = 90
Symmetry Space Group P 1 21 1
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 4 mirrors 2006-05-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 0.933 ESRF ID14-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 50 93.9 0.106 5.9 3.6 65149 65149
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2 2.07 75.6 0.514 1.5 2.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 ID 2o4g 2.1 24.67 57688 51263 2729 95.77 0.21508 0.21336 0.2354 0.2473 0.2603 RANDOM 31.667
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] -0.16 0.1 0.09 0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.816 r_dihedral_angle_3_deg 13.854 r_dihedral_angle_4_deg 10.573 r_dihedral_angle_1_deg 5.117 r_angle_refined_deg 1.056 r_scangle_it 0.946 r_scbond_it 0.561 r_mcangle_it 0.465 r_metal_ion_refined 0.32 r_nbtor_refined 0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.816 r_dihedral_angle_3_deg 13.854 r_dihedral_angle_4_deg 10.573 r_dihedral_angle_1_deg 5.117 r_angle_refined_deg 1.056 r_scangle_it 0.946 r_scbond_it 0.561 r_mcangle_it 0.465 r_metal_ion_refined 0.32 r_nbtor_refined 0.29 r_mcbond_it 0.264 r_nbd_refined 0.173 r_xyhbond_nbd_refined 0.126 r_symmetry_vdw_refined 0.124 r_symmetry_hbond_refined 0.066 r_chiral_restr 0.063 r_bond_refined_d 0.006 r_gen_planes_refined 0.002 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_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 6736 Nucleic Acid Atoms Solvent Atoms 420 Heterogen Atoms 88
Software Software Software Name Purpose REFMAC refinement ADSC data collection DENZO data reduction SCALEPACK data scaling CNS phasing