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TtX183B - A c-type cytochrome domain from the Teredinibacter turnerae protein TERTU_2913
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other TtX183A model, PDB code not yet avilable
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 292 15-25% (w/v) PEG 6000, 200 mM sodium acetate pH 5.0 and 200 mM NaCl
Crystal Properties Matthews coefficient Solvent content 2.29 46.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.548 α = 90.48 b = 38.659 β = 90.591 c = 44.049 γ = 94.481
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 2019-05-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.96884 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 1.8 38.54 96.8 0.202 0.286 0.202 0.816 3.4 2.3 22802
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 1.8 1.84 0.765 1.082 0.765 0.562 2.2
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 1.8 38.457 22802 1135 96.844 0.197 0.195 0.1993 0.2404 0.2446 12.22
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] 0.158 -0.284 -0.748 0.033 -0.832 -0.113
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.376 r_dihedral_angle_6_deg 14.173 r_dihedral_angle_1_deg 5.984 r_lrange_it 3.621 r_lrange_other 3.606 r_angle_refined_deg 2.4 r_scangle_other 2.341 r_scangle_it 2.34 r_dihedral_angle_2_deg 2.216 r_mcangle_it 1.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.376 r_dihedral_angle_6_deg 14.173 r_dihedral_angle_1_deg 5.984 r_lrange_it 3.621 r_lrange_other 3.606 r_angle_refined_deg 2.4 r_scangle_other 2.341 r_scangle_it 2.34 r_dihedral_angle_2_deg 2.216 r_mcangle_it 1.52 r_mcangle_other 1.52 r_scbond_it 1.425 r_scbond_other 1.409 r_mcbond_it 0.902 r_mcbond_other 0.894 r_angle_other_deg 0.54 r_nbd_refined 0.332 r_symmetry_nbd_other 0.203 r_nbd_other 0.176 r_nbtor_refined 0.175 r_xyhbond_nbd_refined 0.155 r_symmetry_xyhbond_nbd_refined 0.115 r_symmetry_nbtor_other 0.074 r_symmetry_nbd_refined 0.072 r_chiral_restr 0.062 r_gen_planes_other 0.011 r_bond_refined_d 0.01 r_gen_planes_refined 0.01 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1745 Nucleic Acid Atoms Solvent Atoms 139 Heterogen Atoms 134
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Aimless data scaling PHASER phasing XDS data reduction