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Crystal structure of Equine Serum Albumin complex with ibuprofen
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5V0V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 289 1 ul of 36 mg/ml protein in 10 mM Tris pH 7.5 and 150 mM NaCl buffer was mixed with 1 ul of the well condition (0.2 M Li2SO4, 0.1 M Tris:HCl, 2.4 M (NH4)2SO4 final pH 7.4) and equilibrated against well solution in 15 Well Crystallization Plate (Qiagen). Ibuprofen powder was added to the crystallization drop.
Crystal Properties Matthews coefficient Solvent content 2.84 56.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.232 α = 90 b = 95.232 β = 90 c = 141.939 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 PIXEL DECTRIS PILATUS3 6M 2015-10-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.9793 APS 19-ID
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 2.25 50 99.7 0.111 0.116 0.035 0.996 9 10.7 34270 -3
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 2.25 2.29 97 1.117 1.202 0.427 0.675 1.13 6.6
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 5v0v 2.25 47.66 27866 1507 85.3 0.1934 0.191 0.1943 0.2376 0.2361 RANDOM 43.97
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] 0.12 0.06 0.12 -0.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.157 r_dihedral_angle_4_deg 14.484 r_dihedral_angle_3_deg 13.783 r_dihedral_angle_1_deg 5.103 r_angle_refined_deg 1.148 r_angle_other_deg 1.139 r_chiral_restr 0.048 r_gen_planes_refined 0.003 r_bond_refined_d 0.002 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.157 r_dihedral_angle_4_deg 14.484 r_dihedral_angle_3_deg 13.783 r_dihedral_angle_1_deg 5.103 r_angle_refined_deg 1.148 r_angle_other_deg 1.139 r_chiral_restr 0.048 r_gen_planes_refined 0.003 r_bond_refined_d 0.002 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4568 Nucleic Acid Atoms Solvent Atoms 266 Heterogen Atoms 100
Software Software Software Name Purpose REFMAC refinement HKL-3000 data scaling PDB_EXTRACT data extraction HKL-3000 data collection Coot model building HKL-3000 data reduction MOLREP phasing