4ZXR

Structure of Thaumatin wrapped in graphene within vacuum


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1KWN 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.8293Commercial 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 coefficientSolvent content
2.9758.56

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.079α = 90
b = 59.079β = 90
c = 151.22γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray295PIXELDECTRIS PILATUS 6M2014-11-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.9795DiamondI04

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.9241.7895.90.0590.0340.99810.63.620125
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)RedundancyNumber Unique Reflections (All)
11.921.9798.80.580.3410.74523.61390

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1KWN1.9241.781914398294.440.14760.14620.1748RANDOM37.326
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]
-0.1-0.10.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.535
r_dihedral_angle_4_deg22.37
r_dihedral_angle_3_deg12.319
r_dihedral_angle_1_deg6.996
r_mcangle_it3.089
r_angle_refined_deg2.182
r_mcbond_it2.053
r_mcbond_other2.049
r_angle_other_deg1.155
r_chiral_restr0.399
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.535
r_dihedral_angle_4_deg22.37
r_dihedral_angle_3_deg12.319
r_dihedral_angle_1_deg6.996
r_mcangle_it3.089
r_angle_refined_deg2.182
r_mcbond_it2.053
r_mcbond_other2.049
r_angle_other_deg1.155
r_chiral_restr0.399
r_bond_refined_d0.022
r_gen_planes_refined0.01
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1512
Nucleic Acid Atoms
Solvent Atoms87
Heterogen Atoms22

Software

Software
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction