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Crystal structure of a poplar wild-type thioredoxin h, PtTrxh4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other SeMet Model solved using SAD method
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 microbatch under oil 7.5 293 0.1 M Na HEPES (pH 7.5), 30 % (w/v) PEG 4000, 0.2 M CaCl2) with 1 mM DTT added to the initial protein solution, microbatch under oil, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.02 39.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.355 α = 90 b = 47.355 β = 90 c = 195.996 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MAR CCD 165 mm mirrors 2005-03-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 0.8123 EMBL/DESY, HAMBURG X11
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 2.15 50 99.8 0.053 22.9 13453 13453
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) 2.15 2.23 100 0.392 2.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 SeMet Model solved using SAD method 2.15 41 13385 13385 660 99.8 0.213 0.213 0.21 0.2067 0.285 0.2798 RANDOM 56.534
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] -1.32 -0.66 -1.32 1.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.759 r_dihedral_angle_3_deg 22.483 r_dihedral_angle_4_deg 21.56 r_dihedral_angle_1_deg 7.6 r_scangle_it 5.099 r_scbond_it 3.766 r_mcangle_it 2.854 r_angle_refined_deg 2.53 r_mcbond_it 1.814 r_symmetry_hbond_refined 0.421
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.759 r_dihedral_angle_3_deg 22.483 r_dihedral_angle_4_deg 21.56 r_dihedral_angle_1_deg 7.6 r_scangle_it 5.099 r_scbond_it 3.766 r_mcangle_it 2.854 r_angle_refined_deg 2.53 r_mcbond_it 1.814 r_symmetry_hbond_refined 0.421 r_nbtor_refined 0.327 r_nbd_refined 0.256 r_chiral_restr 0.23 r_symmetry_vdw_refined 0.23 r_xyhbond_nbd_refined 0.198 r_bond_refined_d 0.031 r_gen_planes_refined 0.013
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1780 Nucleic Acid Atoms Solvent Atoms 62 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection MOLREP phasing