2BK0

Crystal structure of the major celery allergen Api G 1


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1BV1PDB ENTRY 1BV1

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION6.5VAPOUR DIFFUSION. RESERVOIR: 10% DIOXANE, 0.1M MES (PH 6.5), 1.6 M AMMONIUM SULFATE. PROTEIN: 35MG/ML IN 28 MM SODIUM PHOSPHATE (PH 7.0).
Crystal Properties
Matthews coefficientSolvent content
2.535.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 105.878α = 90
b = 67.947β = 91.18
c = 48.001γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray277IMAGE PLATEMAR scanner 345 mm plateOSMICSMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEROTATING GENERATOR

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
12.836.9690.10.098.31.657549
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)
12.82.83930.391.361.59

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 1BV12.9306567315900.2240.2210.269RANDOM21.99
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]
-1.970.844.53-2.52
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.961
r_dihedral_angle_4_deg24.267
r_dihedral_angle_3_deg19.527
r_dihedral_angle_1_deg5.761
r_angle_refined_deg1.053
r_angle_other_deg0.941
r_scangle_it0.575
r_symmetry_hbond_refined0.378
r_scbond_it0.346
r_mcangle_it0.274
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.961
r_dihedral_angle_4_deg24.267
r_dihedral_angle_3_deg19.527
r_dihedral_angle_1_deg5.761
r_angle_refined_deg1.053
r_angle_other_deg0.941
r_scangle_it0.575
r_symmetry_hbond_refined0.378
r_scbond_it0.346
r_mcangle_it0.274
r_mcbond_it0.243
r_nbd_refined0.189
r_nbd_other0.179
r_nbtor_refined0.169
r_symmetry_vdw_other0.162
r_xyhbond_nbd_refined0.148
r_symmetry_vdw_refined0.109
r_chiral_restr0.102
r_nbtor_other0.085
r_bond_refined_d0.008
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other0.001
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2280
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing