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TtX122B - A domain of unknown function from the Teredinibacter turnerae protein TERTU_2913
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Structure of TtX122A currently also being deposited
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 292 0.2 M NaCl, 25% PEG3350 and 0.1 M Bis-Tris pH 6.5
Crystal Properties Matthews coefficient Solvent content 34.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.141 α = 90 b = 75.324 β = 90 c = 116.863 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 PILATUS3 6M 2018-09-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.96863 Diamond I24
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 2.2 46.69 99.8 0.365 0.432 0.228 0.601 6.2 6.8 31699
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 2.2 2.27 2.304 2.805 1.568 0.726 5.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.2 46.69 31624 1583 99.694 0.211 0.2085 0.2085 0.259 0.2572 14.89
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] -1.366 1.98 -0.614
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.57 r_dihedral_angle_3_deg 15.435 r_dihedral_angle_2_deg 8.922 r_dihedral_angle_1_deg 8.816 r_lrange_it 6.288 r_lrange_other 6.276 r_scangle_it 5.058 r_scangle_other 5.057 r_mcangle_it 3.387 r_mcangle_other 3.387
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.57 r_dihedral_angle_3_deg 15.435 r_dihedral_angle_2_deg 8.922 r_dihedral_angle_1_deg 8.816 r_lrange_it 6.288 r_lrange_other 6.276 r_scangle_it 5.058 r_scangle_other 5.057 r_mcangle_it 3.387 r_mcangle_other 3.387 r_scbond_it 3.326 r_scbond_other 3.325 r_mcbond_it 2.249 r_mcbond_other 2.248 r_angle_refined_deg 2.031 r_angle_other_deg 0.723 r_symmetry_xyhbond_nbd_refined 0.213 r_nbd_other 0.211 r_symmetry_nbd_other 0.207 r_nbd_refined 0.203 r_nbtor_refined 0.189 r_xyhbond_nbd_refined 0.186 r_symmetry_nbd_refined 0.179 r_metal_ion_refined 0.148 r_ncsr_local_group_1 0.12 r_ncsr_local_group_2 0.116 r_ncsr_local_group_3 0.11 r_chiral_restr 0.102 r_symmetry_nbtor_other 0.094 r_bond_refined_d 0.016 r_gen_planes_refined 0.012 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5329 Nucleic Acid Atoms Solvent Atoms 163 Heterogen Atoms 3
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PHASER phasing XDS data reduction