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Crystal structure of a Candidatus photodesmus katoptron thioredoxin chimera containing an ancestral loop
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2TRX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 HAMPTON RESEARCH:
HRI: C33 & C34
PEG-ION: C13
Crystal Properties Matthews coefficient Solvent content 4.71 73.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 140.08 α = 90 b = 140.08 β = 90 c = 140.08 γ = 90
Symmetry Space Group I 21 3
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 PILATUS 6M 2017-10-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.9686 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.85 44.33 99.48 0.121 0.074 0.994 7.67 3.5 19411 82.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.85 2.93 99.91 0.935 0.557 0.454 1.03 3.7
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 2TRX 2.85 44.3 1.01 19411 962 93.4 0.2627 0.2613 0.2636 0.2867 0.2888 71.61
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 10.9236 f_angle_d 0.6885 f_chiral_restr 0.0467 f_plane_restr 0.0042 f_bond_d 0.0034
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1648 Nucleic Acid Atoms Solvent Atoms 12 Heterogen Atoms 63
Software Software Software Name Purpose XDS data reduction MOLREP phasing PHENIX refinement PDB_EXTRACT data extraction Aimless data scaling