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Crystal structure of the third thioredoxin domain of human ERp46
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DIZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 288 0.1 M HEPES, 20 % (w/v) PEG 10.000, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 288K
Crystal Properties Matthews coefficient Solvent content 3.27 62.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.58 α = 90 b = 63.58 β = 90 c = 68.68 γ = 120
Symmetry Space Group P 32 2 1
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 2010-10-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.91841 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.651 55.062 99.1 0.093 15.6 8.1 4858 4858 3 61.4
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 2.65 2.79 99.1 0.47 0.47 1.6 8.3 688
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2DIZ 2.651 55.062 4841 239 98.27 0.2303 0.2287 0.2371 0.2591 0.243 RANDOM 55.2571
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] 26.58 26.58 -53.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.052 r_dihedral_angle_3_deg 21.887 r_dihedral_angle_4_deg 18.013 r_dihedral_angle_1_deg 7.016 r_scangle_it 3.702 r_scbond_it 2.206 r_angle_refined_deg 1.792 r_mcangle_it 1.325 r_mcbond_it 0.626 r_chiral_restr 0.115
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.052 r_dihedral_angle_3_deg 21.887 r_dihedral_angle_4_deg 18.013 r_dihedral_angle_1_deg 7.016 r_scangle_it 3.702 r_scbond_it 2.206 r_angle_refined_deg 1.792 r_mcangle_it 1.325 r_mcbond_it 0.626 r_chiral_restr 0.115 r_bond_refined_d 0.018 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 775 Nucleic Acid Atoms Solvent Atoms 23 Heterogen Atoms
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction AUTOMAR data collection