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Crystal structure of the major celery allergen Api G 1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BV1 PDB ENTRY 1BV1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.5 VAPOUR 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 coefficient Solvent content 2.5 35.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.878 α = 90 b = 67.947 β = 91.18 c = 48.001 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 277 IMAGE PLATE MAR scanner 345 mm plate OSMICS M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE ROTATING GENERATOR
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.8 36.96 90.1 0.09 8.3 1.65 7549
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.83 93 0.39 1.36 1.59
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1BV1 2.9 30 6567 315 90 0.224 0.221 0.2251 0.269 0.2726 RANDOM 21.99
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] -1.97 0.84 4.53 -2.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.961 r_dihedral_angle_4_deg 24.267 r_dihedral_angle_3_deg 19.527 r_dihedral_angle_1_deg 5.761 r_angle_refined_deg 1.053 r_angle_other_deg 0.941 r_scangle_it 0.575 r_symmetry_hbond_refined 0.378 r_scbond_it 0.346 r_mcangle_it 0.274
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.961 r_dihedral_angle_4_deg 24.267 r_dihedral_angle_3_deg 19.527 r_dihedral_angle_1_deg 5.761 r_angle_refined_deg 1.053 r_angle_other_deg 0.941 r_scangle_it 0.575 r_symmetry_hbond_refined 0.378 r_scbond_it 0.346 r_mcangle_it 0.274 r_mcbond_it 0.243 r_nbd_refined 0.189 r_nbd_other 0.179 r_nbtor_refined 0.169 r_symmetry_vdw_other 0.162 r_xyhbond_nbd_refined 0.148 r_symmetry_vdw_refined 0.109 r_chiral_restr 0.102 r_nbtor_other 0.085 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 Atoms Number Protein Atoms 2280 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling AMoRE phasing