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Crystal Structure of the Dog Lipocalin Allergen Can f 6
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GM6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 1.0 M ammonium dihydrogenphosphate, 20% (w/v) PEG3350
Crystal Properties Matthews coefficient Solvent content 2.43 49.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.604 α = 90 b = 96.604 β = 90 c = 85.601 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RAYONIX MX225HE 2016-05-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1 SPring-8 BL38B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.35 96.6 100 0.101 0.028 0.952 52.2 13.6 32931
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.35 2.39 100 14.3
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 1GM6 2.35 96.6 31249 1657 99.95 0.20607 0.20272 0.2055 0.26882 0.2689 RANDOM 46.849
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] -0.01 -0.01 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.238 r_dihedral_angle_3_deg 14.706 r_dihedral_angle_4_deg 11.444 r_long_range_B_other 8.393 r_long_range_B_refined 8.391 r_dihedral_angle_1_deg 7.317 r_scangle_other 6.561 r_mcangle_it 5.588 r_mcangle_other 5.587 r_scbond_it 4.524
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.238 r_dihedral_angle_3_deg 14.706 r_dihedral_angle_4_deg 11.444 r_long_range_B_other 8.393 r_long_range_B_refined 8.391 r_dihedral_angle_1_deg 7.317 r_scangle_other 6.561 r_mcangle_it 5.588 r_mcangle_other 5.587 r_scbond_it 4.524 r_scbond_other 4.524 r_mcbond_other 3.991 r_mcbond_it 3.99 r_angle_refined_deg 1.822 r_angle_other_deg 1.017 r_chiral_restr 0.106 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5004 Nucleic Acid Atoms Solvent Atoms 75 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection MOLREP phasing REFMAC phasing