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Crystal structure of TREX1 in complex with a Y structured DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3MXM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 293 0.1M SODIUM ACETATE TRIHYDRATE PH 4.5,
30%(V/V) POLYETHYLENE GLYCOL 300, VAPOR DIFFUSION, HANGING DROP,
TEMPERATURE 293K
Crystal Properties Matthews coefficient Solvent content 1.99 38.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.532 α = 90 b = 96.604 β = 90 c = 101.112 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 298 CCD RAYONIX MX225HE 2012-07-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 29.33 97.4 0.074 31.4 6.6 39153
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.07 100 0.487 3.8 6.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3MXM 2 29.33 1.36 38969 3005 97.1 0.192 0.189 0.1912 0.226 0.2263
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 18.763 f_angle_d 0.851 f_chiral_restr 0.032 f_bond_d 0.004 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3569 Nucleic Acid Atoms 748 Solvent Atoms 413 Heterogen Atoms 4
Software Software Software Name Purpose HKL-2000 data scaling MOLREP phasing PHENIX refinement HKL-2000 data reduction