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Structure of TREX1 in complex with a nucleotide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Y97 PDB ENTRY 1Y97
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 22% PEG 3350, 0.1M MES, 0.2M lithium sulfate , pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.28 46.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.183 α = 90 b = 81.459 β = 103.22 c = 93.127 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 2005-09-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.934 ESRF ID14-1
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 2.35 30 98.2 0.068 10 3.9 40389 40389
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) 1 2.35 2.39 87.6 0.232 3.7 3.9 4047
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 (All) 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 1Y97 2.35 30 38687 38687 2033 99.6 0.20587 0.20587 0.20329 0.2061 0.25456 0.257 RANDOM 19.92
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] 1.16 -0.55 -0.51 -0.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.174 r_dihedral_angle_4_deg 17.175 r_dihedral_angle_3_deg 14.441 r_dihedral_angle_1_deg 6.622 r_scangle_it 1.88 r_angle_refined_deg 1.36 r_scbond_it 1.272 r_angle_other_deg 0.901 r_mcangle_it 0.713 r_mcbond_it 0.605
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.174 r_dihedral_angle_4_deg 17.175 r_dihedral_angle_3_deg 14.441 r_dihedral_angle_1_deg 6.622 r_scangle_it 1.88 r_angle_refined_deg 1.36 r_scbond_it 1.272 r_angle_other_deg 0.901 r_mcangle_it 0.713 r_mcbond_it 0.605 r_symmetry_hbond_refined 0.302 r_nbd_refined 0.199 r_nbd_other 0.182 r_xyhbond_nbd_refined 0.171 r_nbtor_refined 0.17 r_symmetry_vdw_other 0.169 r_metal_ion_refined 0.133 r_mcbond_other 0.108 r_symmetry_vdw_refined 0.095 r_nbtor_other 0.086 r_chiral_restr 0.074 r_bond_refined_d 0.01 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6712 Nucleic Acid Atoms Solvent Atoms 190 Heterogen Atoms 92
Software Software Software Name Purpose REFMAC refinement ADSC data collection DENZO data reduction SCALEPACK data scaling MOLREP phasing