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The apo-mTREX1 crystal structure for soaking experiments (Soaking Condition 2)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5YWS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 1.8M Sodium acetate trihydrate pH7.0, 0.1M BIS-TRIS propane pH7.0
Crystal Properties Matthews coefficient Solvent content 2.66 53.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.362 α = 90 b = 83.186 β = 90 c = 88.479 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 100 PIXEL DECTRIS EIGER2 X 16M 2023-12-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE TPS 07A 0.97625 NSRRC TPS 07A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.4 30 99.5 0.049 0.051 0.015 1 12.5 8.8 110147
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.4 1.45 98.3 0.393 0.436 0.183 0.5 4.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 THROUGHOUT 1.4 26.63 1.42 109324 8421 99.55 0.148 0.1458 0.1457 0.175 0.175
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 5.978 f_angle_d 1.15 f_chiral_restr 0.087 f_plane_restr 0.02 f_bond_d 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3453 Nucleic Acid Atoms Solvent Atoms 461 Heterogen Atoms 20
Software Software Software Name Purpose HKL-2000 data reduction HKL-2000 data scaling BALBES phasing PHENIX refinement PDB_EXTRACT data extraction