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1.2 A Structure of Thaumatin Crystallized in Gel
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1THW PDB ENTRY 1THW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICRODIALYSIS 6.5 293 Na-tartrate (0.52M), Na-ADA (0.1M), agarose gel (0.15% m/v).
THE CRYSTALS WERE GROWN IN THE ADVANCED PROTEIN CRYSTALLIZATION
FACILITY (APCF) ABOARD THE US SPACE SHUTTLE (MISSION STS-95) USING
EITHER A DIALYSIS SETUP (3 CRYSTALS) OR A FREE-INTERFACE DIFFUSION
SETUP (1 CRYSTAL)., pH 6.5, Dialysis in APCF reactor, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.92 57.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.53 α = 90 b = 58.53 β = 90 c = 151.35 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 293 IMAGE PLATE MARRESEARCH 1998-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7B 0.8337 EMBL/DESY, HAMBURG BW7B
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 1.2 20 99 0.036 0.036 26.5 7.2 82240 14.3
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 1.2 1.23 97.8 0.522 0.522 2.05 4.6
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 1THW 1.2 19.96 78110 4130 98.96 0.1037 0.103 0.1032 0.1171 0.1172 RANDOM 22.388
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] 0.31 0.31 -0.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.598 r_sphericity_free 18.322 r_sphericity_bonded 18.056 r_dihedral_angle_4_deg 14.16 r_dihedral_angle_3_deg 11.016 r_dihedral_angle_1_deg 6.59 r_rigid_bond_restr 5.525 r_angle_refined_deg 1.5 r_angle_other_deg 0.951 r_chiral_restr 0.099
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.598 r_sphericity_free 18.322 r_sphericity_bonded 18.056 r_dihedral_angle_4_deg 14.16 r_dihedral_angle_3_deg 11.016 r_dihedral_angle_1_deg 6.59 r_rigid_bond_restr 5.525 r_angle_refined_deg 1.5 r_angle_other_deg 0.951 r_chiral_restr 0.099 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1539 Nucleic Acid Atoms Solvent Atoms 235 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling CNS phasing