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Crystal Structure of mTREX1 with ssDNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2IOC PDB ENTRY 2IOC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 22% PEG 3350, 50mM MES, pH 6.5, 50mM HEPES, pH 7.15, 2mM CaCl2, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.25 45.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.85 α = 90 b = 57.141 β = 107.47 c = 68.47 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 IMAGE PLATE RIGAKU mirrors 2006-09-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.54
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 2.1 61.86 99.9 0.05 11.2 3.51 37899 37899
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 2.11 2.22 99.9 0.231 4.1 3.55 3936
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 ENTRY 2IOC 2.1 61.9 26646 1401 99.69 0.19514 0.1919 0.2026 0.25916 0.26 RANDOM 41.719
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] -3.35 -1.13 3.46 -0.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.818 r_dihedral_angle_4_deg 20.968 r_dihedral_angle_3_deg 17.764 r_dihedral_angle_1_deg 7.241 r_scangle_it 3.513 r_scbond_it 2.429 r_angle_refined_deg 1.952 r_mcangle_it 1.543 r_mcbond_it 0.987 r_symmetry_hbond_refined 0.456
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.818 r_dihedral_angle_4_deg 20.968 r_dihedral_angle_3_deg 17.764 r_dihedral_angle_1_deg 7.241 r_scangle_it 3.513 r_scbond_it 2.429 r_angle_refined_deg 1.952 r_mcangle_it 1.543 r_mcbond_it 0.987 r_symmetry_hbond_refined 0.456 r_nbtor_refined 0.304 r_metal_ion_refined 0.267 r_symmetry_vdw_refined 0.234 r_nbd_refined 0.228 r_xyhbond_nbd_refined 0.211 r_chiral_restr 0.137 r_bond_refined_d 0.02 r_gen_planes_refined 0.008 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 3437 Nucleic Acid Atoms 162 Solvent Atoms 288 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection d*TREK data reduction d*TREK data scaling PHASER phasing