6FJ9

Structure of Thaumatin collected from an in situ crystal on ID30B at 17.5 keV.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5A47 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52930.1M HEPES and 0.7 M potassium/sodium tartrate
Crystal Properties
Matthews coefficientSolvent content
2.9358

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.57α = 90
b = 58.57β = 90
c = 151.544γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293PIXELDECTRIS PILATUS3 6MBe CRL (vertical focusing) and Rh stripe Elliptical mirror (horizontal focusing)2016-09-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID30B0.7085ESRFID30B

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)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
11.554.6392.60.0860.1110.0570.997.23.43979412.4
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.51.5396.70.7270.9790.5180.61.33.4

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 REPLACEMENTTHROUGHOUT5a471.554.6337747198592.020.13820.136730.16678RANDOM19.775
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]
0.040.04-0.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.349
r_sphericity_free22.123
r_dihedral_angle_4_deg15.25
r_dihedral_angle_3_deg11.987
r_dihedral_angle_1_deg9.826
r_sphericity_bonded8.756
r_long_range_B_refined2.286
r_long_range_B_other2.284
r_rigid_bond_restr1.975
r_scangle_other1.972
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.349
r_sphericity_free22.123
r_dihedral_angle_4_deg15.25
r_dihedral_angle_3_deg11.987
r_dihedral_angle_1_deg9.826
r_sphericity_bonded8.756
r_long_range_B_refined2.286
r_long_range_B_other2.284
r_rigid_bond_restr1.975
r_scangle_other1.972
r_mcangle_other1.552
r_mcangle_it1.54
r_scbond_other1.529
r_scbond_it1.526
r_angle_refined_deg1.434
r_mcbond_it1.143
r_mcbond_other1.085
r_angle_other_deg0.924
r_chiral_restr0.087
r_bond_refined_d0.01
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1545
Nucleic Acid Atoms
Solvent Atoms121
Heterogen Atoms10

Software

Software
Software NamePurpose
MxCuBEdata collection
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing