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Structure of Thaumatin wrapped in graphene within vacuum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KWN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.8 293 Commercial thaumatin from Thaumatococcus danielli (Sigma-Aldrich) was resuspended in Milli-Q water to a concentration of 40 mg/mL. Sitting drops were made by mixing 4 uL of protein solution and 2 uL of reservoir solution [50 mM N-(2-Acetamido)iminodiacetic acid(ADA) pH 6.8, 600 mM potassium sodium tartrate and 20 % (v/v) Glycerol] and equilibrated against 500 uL of reservoir solution at 293K.
Crystal Properties Matthews coefficient Solvent content 2.97 58.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.079 α = 90 b = 59.079 β = 90 c = 151.22 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 295 PIXEL DECTRIS PILATUS 6M 2014-11-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) 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 1.92 41.78 95.9 0.059 0.034 0.998 10.6 3.6 20125
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.92 1.97 98.8 0.58 0.341 0.745 2 3.6 1390
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 1KWN 1.92 41.78 19143 982 94.44 0.1476 0.1462 0.1578 0.1748 0.1628 RANDOM 37.326
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] -0.1 -0.1 0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.535 r_dihedral_angle_4_deg 22.37 r_dihedral_angle_3_deg 12.319 r_dihedral_angle_1_deg 6.996 r_mcangle_it 3.089 r_angle_refined_deg 2.182 r_mcbond_it 2.053 r_mcbond_other 2.049 r_angle_other_deg 1.155 r_chiral_restr 0.399
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.535 r_dihedral_angle_4_deg 22.37 r_dihedral_angle_3_deg 12.319 r_dihedral_angle_1_deg 6.996 r_mcangle_it 3.089 r_angle_refined_deg 2.182 r_mcbond_it 2.053 r_mcbond_other 2.049 r_angle_other_deg 1.155 r_chiral_restr 0.399 r_bond_refined_d 0.022 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1512 Nucleic Acid Atoms Solvent Atoms 87 Heterogen Atoms 22
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction