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Crystal Structure of cat allergen Fel d 4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold alphafold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 4.5 293.15 0.1 M Sodium acetate trihydrate pH 4.5, 2.0 M Ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.93 58.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.291 α = 90 b = 120.571 β = 106.513 c = 67.149 γ = 90
Symmetry Space Group P 1 21 1
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 PILATUS 6M 2021-02-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.873128 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.95 34.11 99.61 0.145 0.173 0.094 0.993 9.8 6.5 21622
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.95 3.055 0.828 0.983 0.523 0.722 6.7
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE alphafold 2.95 34.11 21618 1063 99.627 0.181 0.1787 0.1784 0.2299 0.2297 62.645
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] -0.904 0.59 0.147 0.347
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.722 r_dihedral_angle_4_deg 18.978 r_lrange_it 14.184 r_lrange_other 14.173 r_dihedral_angle_3_deg 13.905 r_scangle_it 9.759 r_scangle_other 9.725 r_mcangle_it 8.867 r_mcangle_other 8.859 r_dihedral_angle_1_deg 8.159
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.722 r_dihedral_angle_4_deg 18.978 r_lrange_it 14.184 r_lrange_other 14.173 r_dihedral_angle_3_deg 13.905 r_scangle_it 9.759 r_scangle_other 9.725 r_mcangle_it 8.867 r_mcangle_other 8.859 r_dihedral_angle_1_deg 8.159 r_scbond_it 6.073 r_scbond_other 6.052 r_mcbond_it 5.62 r_mcbond_other 5.612 r_angle_refined_deg 1.74 r_angle_other_deg 1.276 r_symmetry_nbd_refined 0.792 r_symmetry_xyhbond_nbd_refined 0.773 r_xyhbond_nbd_other 0.584 r_nbd_other 0.524 r_nbd_refined 0.207 r_symmetry_nbd_other 0.191 r_ext_dist_refined_d 0.158 r_nbtor_refined 0.158 r_xyhbond_nbd_refined 0.154 r_ncsr_local_group_3 0.148 r_ncsr_local_group_5 0.139 r_ncsr_local_group_4 0.136 r_ncsr_local_group_2 0.134 r_ncsr_local_group_1 0.13 r_ncsr_local_group_6 0.128 r_chiral_restr 0.092 r_symmetry_nbtor_other 0.078 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5138 Nucleic Acid Atoms Solvent Atoms 99 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement REFMAC refinement PHASER phasing Aimless data scaling XDS data reduction