4A83

Crystal Structure of Major Birch Pollen Allergen Bet v 1 a in complex with deoxycholate.


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
1.9938.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 32.6α = 90
b = 56.12β = 93.58
c = 38.07γ = 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
11.543898.30.0419.33.720001
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)
11.541.6288.80.099.73.2

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 4A801.543818973101198.270.125090.122820.16819RANDOM13.384
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]
-0.110.340.35-0.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.267
r_dihedral_angle_4_deg34.027
r_sphericity_free33.945
r_dihedral_angle_3_deg12.195
r_sphericity_bonded8.986
r_dihedral_angle_1_deg5.909
r_scangle_it5.484
r_scbond_it3.567
r_mcangle_it2.498
r_rigid_bond_restr2.311
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.267
r_dihedral_angle_4_deg34.027
r_sphericity_free33.945
r_dihedral_angle_3_deg12.195
r_sphericity_bonded8.986
r_dihedral_angle_1_deg5.909
r_scangle_it5.484
r_scbond_it3.567
r_mcangle_it2.498
r_rigid_bond_restr2.311
r_angle_refined_deg1.485
r_mcbond_it1.438
r_angle_other_deg0.837
r_mcbond_other0.361
r_symmetry_vdw_refined0.274
r_nbd_refined0.26
r_symmetry_hbond_refined0.258
r_symmetry_vdw_other0.221
r_nbd_other0.199
r_xyhbond_nbd_refined0.188
r_nbtor_refined0.177
r_chiral_restr0.088
r_nbtor_other0.086
r_bond_refined_d0.009
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 Atoms1232
Nucleic Acid Atoms
Solvent Atoms140
Heterogen Atoms89

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing