4A88

Crystal Structure of native Major Birch Pollen Allergen Bet v 1 isoform a


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4A80PDB ENTRY 4A80

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17pH 7
Crystal Properties
Matthews coefficientSolvent content
1.9537.06

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 32.61α = 90
b = 55.4β = 93.05
c = 37.89γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDMIRRORS2010-08-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.1BESSY14.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.5137.8497.90.0516.73.620772
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)
11.511.5985.60.136.62.8

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 ENTRY 4A801.5137.8419696105997.80.114070.11120.16792RANDOM13.695
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]
-0.110.20.31-0.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.659
r_sphericity_free37.637
r_dihedral_angle_4_deg30.571
r_dihedral_angle_3_deg12.229
r_sphericity_bonded11.415
r_dihedral_angle_1_deg5.818
r_rigid_bond_restr2.687
r_angle_refined_deg1.453
r_angle_other_deg0.908
r_chiral_restr0.101
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.659
r_sphericity_free37.637
r_dihedral_angle_4_deg30.571
r_dihedral_angle_3_deg12.229
r_sphericity_bonded11.415
r_dihedral_angle_1_deg5.818
r_rigid_bond_restr2.687
r_angle_refined_deg1.453
r_angle_other_deg0.908
r_chiral_restr0.101
r_bond_refined_d0.012
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_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1229
Nucleic Acid Atoms
Solvent Atoms215
Heterogen Atoms51

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing