2VXQ

Crystal structure of the major grass pollen allergen Phl p 2 in complex with its specific IgE-Fab


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.8HANGING DROP DIFFUSION, 1 MICROL PROTEIN (IN 30 MM HEPES, 0.15 M NACL PH 6.8) MIXED WITH 1 MICROL RESERVOIR (20% PEG 3350, 0.2 M NAF)
Crystal Properties
Matthews coefficientSolvent content
2.550

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 105.437α = 90
b = 105.437β = 90
c = 110.225γ = 90
Symmetry
Space GroupP 42 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2007-07-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SASLSX06SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)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
11.927.5698.40.0770.0717.895.5348722
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.91.9289.50.242.434.34

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 REPLACEMENTTHROUGHOUTPDB ENTRIES 1U6A, 1WH01.93048678246698.30.1790.1770.226RANDOM21.76
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]
-0.08-0.080.159
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.473
r_dihedral_angle_4_deg19.1
r_dihedral_angle_3_deg11.889
r_scangle_it8.44
r_scbond_it7.189
r_dihedral_angle_1_deg7.088
r_mcangle_it5.362
r_mcbond_it4.763
r_angle_refined_deg1.22
r_angle_other_deg0.783
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.473
r_dihedral_angle_4_deg19.1
r_dihedral_angle_3_deg11.889
r_scangle_it8.44
r_scbond_it7.189
r_dihedral_angle_1_deg7.088
r_mcangle_it5.362
r_mcbond_it4.763
r_angle_refined_deg1.22
r_angle_other_deg0.783
r_symmetry_hbond_refined0.291
r_symmetry_vdw_refined0.251
r_symmetry_vdw_other0.225
r_nbd_other0.2
r_nbd_refined0.193
r_nbtor_refined0.178
r_xyhbond_nbd_refined0.145
r_nbtor_other0.085
r_chiral_restr0.07
r_bond_refined_d0.008
r_bond_other_d0.003
r_gen_planes_refined0.003
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3967
Nucleic Acid Atoms
Solvent Atoms524
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing