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Structure of TREX1 in complex with a nucleotide and inhibitor ions (sodium and zinc)
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 Crystallization: 22% PEG3350, 100 mM MES pH 6.0, 200 mM Li2SO4. Soaking: 24h, 22% PEG3350, 100 mM MES pH 6.0, 50 mM Li2SO4, 200 mM Na2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.26 45.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.772 α = 90 b = 81.496 β = 103.11 c = 92.539 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 2.2 50 98.2 0.118 5.1 3.4 48939 48939
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 2.28 85.9 0.486 1.3 2.5
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 2.3 24.18 45825 40809 2155 99.76 0.24765 0.24564 0.2644 0.28541 0.3033 RANDOM 29.1
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] 0.23 0.07 0.04 -0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.429 r_dihedral_angle_3_deg 13.027 r_dihedral_angle_4_deg 8.67 r_dihedral_angle_1_deg 4.397 r_angle_refined_deg 0.939 r_scangle_it 0.365 r_nbtor_refined 0.284 r_mcangle_it 0.212 r_scbond_it 0.205 r_nbd_refined 0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.429 r_dihedral_angle_3_deg 13.027 r_dihedral_angle_4_deg 8.67 r_dihedral_angle_1_deg 4.397 r_angle_refined_deg 0.939 r_scangle_it 0.365 r_nbtor_refined 0.284 r_mcangle_it 0.212 r_scbond_it 0.205 r_nbd_refined 0.15 r_mcbond_it 0.115 r_symmetry_vdw_refined 0.107 r_metal_ion_refined 0.087 r_xyhbond_nbd_refined 0.078 r_symmetry_hbond_refined 0.065 r_chiral_restr 0.052 r_bond_refined_d 0.005 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 471 Heterogen Atoms 92
Software Software Software Name Purpose REFMAC refinement ADSC data collection DENZO data reduction SCALEPACK data scaling CNS phasing