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Crystal structure of HSA in complex with AmpHecy
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6M5D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 291.15 0.05 M KH2PO4, pH 7.0, 25% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.18 43.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.163 α = 74.45 b = 58.406 β = 88.13 c = 95.479 γ = 76.18
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 EIGER2 S 9M 2024-05-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL02U1 0.97918 SSRF BL02U1
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 3.05 91.93 99 0.147 0.173 0.09 0.989 5.7 3.5 22166
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 3.05 3.26 98.3 0.508 0.603 0.32 0.863 2
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3.05 91.93 20962 1150 98.79 0.29252 0.29006 0.2966 0.3403 0.3444 RANDOM 60.07
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] 6.63 -3.35 -5.51 -3.76 3.49 -1.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.985 r_dihedral_angle_3_deg 16.717 r_dihedral_angle_4_deg 14.282 r_long_range_B_refined 8.411 r_long_range_B_other 8.41 r_mcangle_it 5.641 r_mcangle_other 5.641 r_dihedral_angle_1_deg 5.111 r_scangle_other 4.968 r_mcbond_it 3.407
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.985 r_dihedral_angle_3_deg 16.717 r_dihedral_angle_4_deg 14.282 r_long_range_B_refined 8.411 r_long_range_B_other 8.41 r_mcangle_it 5.641 r_mcangle_other 5.641 r_dihedral_angle_1_deg 5.111 r_scangle_other 4.968 r_mcbond_it 3.407 r_mcbond_other 3.402 r_scbond_it 2.885 r_scbond_other 2.885 r_angle_other_deg 1.413 r_angle_refined_deg 1.011 r_chiral_restr 0.058 r_bond_refined_d 0.004 r_gen_planes_refined 0.003 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 9096 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing