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Crystal structure of cod allergen Gad m 1.0201 coordinating lanthanum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5CPV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 1.9 M sodium malonate pH 5.0
Crystal Properties Matthews coefficient Solvent content 2.39 48.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.712 α = 90 b = 85.723 β = 90 c = 54.786 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER X 16M 2023-03-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0000 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.65 40 92.8 0.157 0.157 0.18 0.084 0.989 13.9 4.5 12683
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.65 1.68 0.422 0.422 0.515 0.284 0.745 2.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.65 33.781 12637 637 92.851 0.164 0.1623 0.1705 0.1967 0.2022 20.282
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] 0.367 0.39 -0.756
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.217 r_dihedral_angle_3_deg 12.518 r_lrange_it 5.526 r_lrange_other 5.219 r_dihedral_angle_1_deg 5.167 r_dihedral_angle_2_deg 3.452 r_scangle_other 3.305 r_scangle_it 3.299 r_scbond_other 2.073 r_scbond_it 2.069
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.217 r_dihedral_angle_3_deg 12.518 r_lrange_it 5.526 r_lrange_other 5.219 r_dihedral_angle_1_deg 5.167 r_dihedral_angle_2_deg 3.452 r_scangle_other 3.305 r_scangle_it 3.299 r_scbond_other 2.073 r_scbond_it 2.069 r_mcangle_it 1.568 r_mcangle_other 1.567 r_angle_refined_deg 1.455 r_mcbond_it 1.118 r_mcbond_other 1.117 r_angle_other_deg 0.532 r_symmetry_nbd_refined 0.388 r_nbd_refined 0.257 r_symmetry_nbd_other 0.196 r_nbtor_refined 0.185 r_symmetry_xyhbond_nbd_refined 0.182 r_xyhbond_nbd_refined 0.148 r_symmetry_metal_ion_refined 0.141 r_nbd_other 0.129 r_metal_ion_refined 0.114 r_symmetry_nbtor_other 0.074 r_chiral_restr 0.071 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 808 Nucleic Acid Atoms Solvent Atoms 196 Heterogen Atoms 17
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-3000 data scaling MOLREP phasing