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Atomic resolution (0.98 A) structure of purified thaumatin I grown in sodium DL-tartrate at 20 C
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KWN PDB ENTRY 1KWN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 7.1 293 MICROBATCH METHOD; PROTEIN AT 45 MG/ML IN 10MM SODIUM PHOSPHATE WITH 0.25M SODIUM DL-TARTRATE (PH=7.1) AND 10% (V/V) GLYCEROL; CRYSTALS GROWN AT 20 C
Crystal Properties Matthews coefficient Solvent content 2.2 42.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.849 α = 90 b = 57.849 β = 90 c = 149.978 γ = 90
Symmetry Space Group P 41 21 2
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 ADSC CCD TOROIDAL FOCUSING MIRROR 2007-08-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X6A NSLS X6A
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 0.98 20 99.2 0.06 37.8 10.4 145126 2
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) 1 0.98 1 99.1 0.53 2.1 5
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 PDB ENTRY 1KWN 0.98 20 137762 7256 99.2 0.125 0.124 0.1288 0.134 0.1364 RANDOM 11.19
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] 0.11 0.11 -0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.259 r_dihedral_angle_4_deg 13.261 r_dihedral_angle_3_deg 10.351 r_dihedral_angle_1_deg 6.738 r_scangle_it 3.219 r_scbond_it 2.406 r_mcangle_it 1.985 r_angle_refined_deg 1.525 r_mcbond_it 1.351 r_nbtor_refined 0.314
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.259 r_dihedral_angle_4_deg 13.261 r_dihedral_angle_3_deg 10.351 r_dihedral_angle_1_deg 6.738 r_scangle_it 3.219 r_scbond_it 2.406 r_mcangle_it 1.985 r_angle_refined_deg 1.525 r_mcbond_it 1.351 r_nbtor_refined 0.314 r_nbd_refined 0.283 r_symmetry_vdw_refined 0.197 r_symmetry_hbond_refined 0.174 r_xyhbond_nbd_refined 0.138 r_chiral_restr 0.095 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1545 Nucleic Acid Atoms Solvent Atoms 353 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing