4A87

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


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
1.9637.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 32.65α = 90
b = 55.42β = 93.28
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
11.2425.2497.90.0612.73.637419
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)
11.241.3188.40.175.22.8

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 4A801.2437.8335510189297.820.128260.12640.16238RANDOM14.134
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]
0.5-0.250.76-1.29
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free39.156
r_dihedral_angle_2_deg36.479
r_dihedral_angle_4_deg31.394
r_sphericity_bonded13.471
r_dihedral_angle_3_deg12.535
r_scangle_it6.338
r_dihedral_angle_1_deg5.518
r_scbond_it4.141
r_rigid_bond_restr3.485
r_mcangle_it3.186
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free39.156
r_dihedral_angle_2_deg36.479
r_dihedral_angle_4_deg31.394
r_sphericity_bonded13.471
r_dihedral_angle_3_deg12.535
r_scangle_it6.338
r_dihedral_angle_1_deg5.518
r_scbond_it4.141
r_rigid_bond_restr3.485
r_mcangle_it3.186
r_mcbond_it2.035
r_angle_refined_deg1.698
r_angle_other_deg0.926
r_symmetry_vdw_refined0.293
r_nbd_refined0.284
r_symmetry_vdw_other0.238
r_nbd_other0.204
r_xyhbond_nbd_refined0.2
r_symmetry_hbond_refined0.2
r_metal_ion_refined0.198
r_nbtor_refined0.188
r_chiral_restr0.109
r_nbtor_other0.09
r_bond_refined_d0.014
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1225
Nucleic Acid Atoms
Solvent Atoms191
Heterogen Atoms67

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing