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Structure of the UHM domain of Puf60 fused to thioredoxin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2TRX 8 thioredoxin domains: PDB entry 2TRX 8 Puf60-UHM domains: homology model based on PDB 2pe8 experimental model PDB 2PE8 8 thioredoxin domains: PDB entry 2TRX 8 Puf60-UHM domains: homology model based on PDB 2pe8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 1.4M ammonium sulfate, 0.05M K-formate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.55 51.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.12 α = 90 b = 89.43 β = 90 c = 299.39 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 CCD MARMOSAIC 225 mm CCD LN2 cooled fixed-exit
Si(111) monochromator
Dynamically bendable mirror
Beamline suitable for large unit cell structures 2007-05-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.006 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.2 49.832 99.8 0.11 0.106 14.53 6.1 103128 102916 1 1 36.481
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.33 98.9 0.393 0.604 3.24 5.8 16266
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) 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 8 thioredoxin domains: PDB entry 2TRX
8 Puf60-UHM domains: homology model based on PDB 2pe8 2.2 49.75 2 103128 102916 5181 99.8 0.21419 0.21419 0.2112 0.2334 0.27148 0.2757 RANDOM 21.623
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] 1.99 -1.26 -0.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.874 r_dihedral_angle_4_deg 17.097 r_dihedral_angle_3_deg 15.816 r_dihedral_angle_1_deg 5.682 r_angle_refined_deg 1.012 r_scangle_it 0.921 r_scbond_it 0.597 r_mcangle_it 0.432 r_mcbond_it 0.341 r_nbtor_refined 0.298
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.874 r_dihedral_angle_4_deg 17.097 r_dihedral_angle_3_deg 15.816 r_dihedral_angle_1_deg 5.682 r_angle_refined_deg 1.012 r_scangle_it 0.921 r_scbond_it 0.597 r_mcangle_it 0.432 r_mcbond_it 0.341 r_nbtor_refined 0.298 r_nbd_refined 0.191 r_symmetry_vdw_refined 0.148 r_xyhbond_nbd_refined 0.13 r_symmetry_hbond_refined 0.107 r_chiral_restr 0.066 r_bond_refined_d 0.006 r_gen_planes_refined 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13074 Nucleic Acid Atoms Solvent Atoms 1191 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection XDS data reduction XDS data scaling PHASER phasing