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Crystal structure of human serum albumin in complex with ALB8(VHH) domain of ozoralizumab
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1AO6 experimental model PDB 1I3V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 4.7 293 100 mM SPG Buffer (pH4.7)
21 % PEG1500
Crystal Properties Matthews coefficient Solvent content 2.51 50.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.29 α = 89.51 b = 60.9 β = 63.72 c = 62.81 γ = 76.49
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 9M 2023-07-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL32XU 1.00000 SPring-8 BL32XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.05 45.3 97.6 0.994 7.09 3.9 47566
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.05 2.17 0.554
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.05 45.3 45167 2399 97.88 0.20432 0.20242 0.23854 0.2447 RANDOM 42.08
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] -0.8 -2.21 1.81 1.69 0.41 -0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.428 r_dihedral_angle_4_deg 22.72 r_dihedral_angle_3_deg 17.539 r_long_range_B_refined 8.458 r_long_range_B_other 8.451 r_dihedral_angle_1_deg 6.238 r_scangle_other 6.026 r_mcangle_it 4.133 r_mcangle_other 4.133 r_scbond_it 3.936
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.428 r_dihedral_angle_4_deg 22.72 r_dihedral_angle_3_deg 17.539 r_long_range_B_refined 8.458 r_long_range_B_other 8.451 r_dihedral_angle_1_deg 6.238 r_scangle_other 6.026 r_mcangle_it 4.133 r_mcangle_other 4.133 r_scbond_it 3.936 r_scbond_other 3.93 r_mcbond_it 2.85 r_mcbond_other 2.849 r_angle_refined_deg 1.518 r_angle_other_deg 1.313 r_chiral_restr 0.079 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 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 5403 Nucleic Acid Atoms Solvent Atoms 127 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing