4A8U

Crystal Structure of native Birch Pollen Allergen Bet v 1 isoform j


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
1.9737.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 32.66α = 90
b = 55.69β = 93.8
c = 38.05γ = 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
11.1618.9898.10.04173.646196
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)
11.161.2288.10.147.33.2

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 4A801.1637.9743861231898.130.120480.119020.14867RANDOM11.008
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]
-0.16-0.030.18-0.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.98
r_dihedral_angle_4_deg35.189
r_sphericity_free32.767
r_scangle_it16.388
r_dihedral_angle_3_deg11.758
r_scbond_it11.663
r_mcangle_it9.009
r_sphericity_bonded8.995
r_mcbond_it6.791
r_dihedral_angle_1_deg5.546
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.98
r_dihedral_angle_4_deg35.189
r_sphericity_free32.767
r_scangle_it16.388
r_dihedral_angle_3_deg11.758
r_scbond_it11.663
r_mcangle_it9.009
r_sphericity_bonded8.995
r_mcbond_it6.791
r_dihedral_angle_1_deg5.546
r_mcbond_other3.381
r_rigid_bond_restr2.293
r_angle_refined_deg1.576
r_angle_other_deg1.098
r_symmetry_vdw_refined0.303
r_nbd_refined0.249
r_symmetry_vdw_other0.237
r_nbd_other0.197
r_chiral_restr0.191
r_nbtor_refined0.181
r_symmetry_hbond_refined0.172
r_xyhbond_nbd_refined0.155
r_nbtor_other0.09
r_bond_refined_d0.01
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.002
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1224
Nucleic Acid Atoms
Solvent Atoms207
Heterogen Atoms78

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing