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Crystal structure of human serum albumin in complex with phosphorodithioate derivative of myristoyl cyclic phosphatidic acid (cPA)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3A73
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 28% PEG3350, 50 mM phosphate buffer
Crystal Properties Matthews coefficient Solvent content 2.2 44.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.895 α = 105.46 b = 85.167 β = 89.78 c = 96.308 γ = 101.34
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 MX-225 2014-05-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.9184 BESSY 14.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.26 46.35 93.5 0.05 12.4 2 49652 -3 44.88
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.26 2.4 90.1 0.369 2.3
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 3A73 2.26 45.9 48640 1012 93.58 0.20734 0.2064 0.2096 0.25262 0.2488 RANDOM 46.163
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] 0.31 0.6 0.06 1.35 0.79 -2.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.142 r_dihedral_angle_4_deg 24.734 r_dihedral_angle_3_deg 18.34 r_long_range_B_refined 7.482 r_long_range_B_other 7.477 r_dihedral_angle_1_deg 6.378 r_scangle_other 5.013 r_mcangle_it 4.336 r_mcangle_other 4.336 r_scbond_it 3.233
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.142 r_dihedral_angle_4_deg 24.734 r_dihedral_angle_3_deg 18.34 r_long_range_B_refined 7.482 r_long_range_B_other 7.477 r_dihedral_angle_1_deg 6.378 r_scangle_other 5.013 r_mcangle_it 4.336 r_mcangle_other 4.336 r_scbond_it 3.233 r_scbond_other 3.232 r_mcbond_other 2.855 r_mcbond_it 2.854 r_angle_refined_deg 1.942 r_angle_other_deg 1.267 r_chiral_restr 0.117 r_bond_refined_d 0.019 r_gen_planes_refined 0.012 r_bond_other_d 0.007 r_gen_planes_other 0.006 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 9260 Nucleic Acid Atoms Solvent Atoms 310 Heterogen Atoms 195
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling