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Crystal structure of equine 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 4OT2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 293 1.8 M Ammonium sulfate, 0.1 M acetate buffer pH 4.5, cocrystallization
Crystal Properties Matthews coefficient Solvent content 2.75 55.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.86 α = 90 b = 93.86 β = 90 c = 141.79 γ = 120
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 2013-04-12 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) 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 2.48 50 99.6 0.088 0.998 14.5 4.6 24973 -3 53.1
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 2.48 2.58 99.4 0.991 2.1 4.7
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 (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 4OT2 2.48 50 23957 1012 99.6 0.17261 0.17031 0.1775 0.22906 0.2294 RANDOM 55.701
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] 0.6 0.3 0.6 -1.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.65 r_dihedral_angle_3_deg 18.395 r_dihedral_angle_4_deg 17.671 r_long_range_B_refined 8.1 r_long_range_B_other 8.096 r_dihedral_angle_1_deg 6.402 r_scangle_other 4.929 r_mcangle_it 3.719 r_mcangle_other 3.719 r_scbond_it 2.999
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.65 r_dihedral_angle_3_deg 18.395 r_dihedral_angle_4_deg 17.671 r_long_range_B_refined 8.1 r_long_range_B_other 8.096 r_dihedral_angle_1_deg 6.402 r_scangle_other 4.929 r_mcangle_it 3.719 r_mcangle_other 3.719 r_scbond_it 2.999 r_scbond_other 2.987 r_mcbond_other 2.318 r_mcbond_it 2.317 r_angle_refined_deg 1.847 r_angle_other_deg 1.038 r_chiral_restr 0.11 r_bond_refined_d 0.02 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 4568 Nucleic Acid Atoms Solvent Atoms 99 Heterogen Atoms 57
Software Software Software Name Purpose REFMAC refinement REFMAC phasing XDS data reduction XSCALE data scaling