7KYW

Crystal structure of timothy grass allergen Phl p 12.0101 reveals an unusual profilin dimer


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION6.52770.5 M sodium citrate at pH 6.5
Crystal Properties
Matthews coefficientSolvent content
3.0559.68

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.344α = 90
b = 56.344β = 90
c = 94.379γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2020-10-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1.0000APS22-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.34099.80.0540.0540.0660.0210.94250.310.48119-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.341000.6980.6980.7660.2380.8252.210.1

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 REPLACEMENTTHROUGHOUT5FEF2.333.94770039599.730.19970.19720.2415RANDOM65.408
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]
-0.88-0.44-0.882.85
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.988
r_dihedral_angle_3_deg11.9
r_dihedral_angle_4_deg8.655
r_dihedral_angle_1_deg5.285
r_angle_other_deg2.294
r_angle_refined_deg1.49
r_chiral_restr0.074
r_bond_other_d0.036
r_bond_refined_d0.014
r_gen_planes_other0.011
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.988
r_dihedral_angle_3_deg11.9
r_dihedral_angle_4_deg8.655
r_dihedral_angle_1_deg5.285
r_angle_other_deg2.294
r_angle_refined_deg1.49
r_chiral_restr0.074
r_bond_other_d0.036
r_bond_refined_d0.014
r_gen_planes_other0.011
r_gen_planes_refined0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms992
Nucleic Acid Atoms
Solvent Atoms16
Heterogen Atoms13

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing