6WGM

Crystal structure of a marine metagenome TRAP solute binding protein specific for pyroglutamate (Sorcerer II Global Ocean Sampling Expedition, unidentified microbe, scf7180008839099) in complex with co-purified pyroglutamate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2PFZ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7292.151.1M Malonic Acid, 0.15 M Ammonium Citrate tribasic, 0.072 M Succinic Acid, 0.18 M DL-Malic Acid, 0.24 M Sodium Acetate, 0.3 M Sodium Formate, 0.096 M Ammonium Tartrate Dibasic
Crystal Properties
Matthews coefficientSolvent content
2.7455.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.251α = 90
b = 56.251β = 90
c = 193.919γ = 120
Symmetry
Space GroupP 61

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX225HEKB MIRRORS2017-11-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 31-ID0.98APS31-ID

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
11.438.91000.110.1150.0340.99812.711.46804114.5
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)
11.41.4299.91.7890.160.5620.78512.811.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2PFZ1.424.361.3567843347699.830.15160.15070.167922.0333
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d6.477
f_angle_d0.754
f_chiral_restr0.073
f_plane_restr0.006
f_bond_d0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2339
Nucleic Acid Atoms
Solvent Atoms298
Heterogen Atoms64

Software

Software
Software NamePurpose
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction