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Structure of TREX1 in complex with DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2O4G PDB ENTRY 2O4G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 20% PEG 2KMME, 0.1M Imidazole, 0.3M lithium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.99 38.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.758 α = 90 b = 80.758 β = 90 c = 171.22 γ = 90
Symmetry Space Group P 43 21 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 4 mirrors 2006-07-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-3 0.931 ESRF ID14-3
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 3.5 25 87.9 0.156 3.7 6.9 6708 6708
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 3.5 3.58 83.6 0.44 1.1 6
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 2O4G 3.5 24.85 6402 6402 321 87.96 0.24516 0.24516 0.24333 0.2374 0.28335 0.2753 RANDOM 96.203
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] -3.41 -3.41 6.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.814 r_dihedral_angle_3_deg 12.426 r_dihedral_angle_4_deg 11.337 r_dihedral_angle_1_deg 4.509 r_angle_refined_deg 1.007 r_angle_other_deg 0.767 r_nbd_refined 0.163 r_nbtor_refined 0.162 r_nbd_other 0.152 r_symmetry_vdw_other 0.152
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.814 r_dihedral_angle_3_deg 12.426 r_dihedral_angle_4_deg 11.337 r_dihedral_angle_1_deg 4.509 r_angle_refined_deg 1.007 r_angle_other_deg 0.767 r_nbd_refined 0.163 r_nbtor_refined 0.162 r_nbd_other 0.152 r_symmetry_vdw_other 0.152 r_scangle_it 0.13 r_symmetry_vdw_refined 0.122 r_xyhbond_nbd_refined 0.096 r_scbond_it 0.085 r_nbtor_other 0.08 r_symmetry_hbond_refined 0.077 r_chiral_restr 0.05 r_mcangle_it 0.044 r_mcbond_it 0.035 r_mcbond_other 0.01 r_bond_refined_d 0.005 r_bond_other_d 0.001 r_gen_planes_refined 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3363 Nucleic Acid Atoms 154 Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement ADSC data collection DENZO data reduction SCALEPACK data scaling MOLREP phasing