4BKC

Crystal Structure of a unusually linked dimeric variant of Bet v 1


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4A88PDB ENTRY 4A88

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.50.1 M NA ACETATE PH 6.5, 27 % PEG 3350
Crystal Properties
Matthews coefficientSolvent content
1.9837.86

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 39.88α = 90
b = 60.95β = 107.47
c = 59.72γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2011-07-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID29ESRFID29

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
11.5541.6298.10.145.7338874
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)
11.551.63981.091.53

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 4A881.7356.9726644142498.140.203550.201240.24672RANDOM19.962
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]
-0.90.421.41-0.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.682
r_dihedral_angle_4_deg29.055
r_sphericity_free19.054
r_dihedral_angle_3_deg11.69
r_mcangle_it5.971
r_sphericity_bonded5.726
r_dihedral_angle_1_deg4.977
r_mcbond_it4.465
r_rigid_bond_restr1.42
r_angle_refined_deg0.906
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.682
r_dihedral_angle_4_deg29.055
r_sphericity_free19.054
r_dihedral_angle_3_deg11.69
r_mcangle_it5.971
r_sphericity_bonded5.726
r_dihedral_angle_1_deg4.977
r_mcbond_it4.465
r_rigid_bond_restr1.42
r_angle_refined_deg0.906
r_nbtor_refined0.307
r_symmetry_vdw_refined0.193
r_nbd_refined0.189
r_symmetry_hbond_refined0.101
r_xyhbond_nbd_refined0.099
r_chiral_restr0.06
r_bond_refined_d0.005
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
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 Atoms2470
Nucleic Acid Atoms
Solvent Atoms219
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing