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Crystal Structure Analysis of Human serum albumin complexed with delta 12-prostaglandin J2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BJ5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 285 50mM phosphate buffer pH 6.5, 28-32% (w/v) PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 285K
Crystal Properties Matthews coefficient Solvent content 2.37 48.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.06 α = 74.8 b = 92.047 β = 89.53 c = 94.664 γ = 80.21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 98 CCD ADSC QUANTUM 315 2008-11-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0000 Photon Factory BL-5A
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 2.19 35.08 92 0.072 14.2 3.6 68079 62497 2 1 37
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.28 91.9 0.113 0.118 4496 3.4 5755
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 1BJ5 2.19 35 59063 54279 2871 91.34 0.23252 0.2294 0.2404 0.2908 0.2703 RANDOM 30.488
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] -1.4 -0.47 0.04 1.69 -2.17 1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.927 r_dihedral_angle_3_deg 21.171 r_dihedral_angle_4_deg 19.553 r_dihedral_angle_1_deg 6.345 r_scangle_it 4.158 r_scbond_it 2.704 r_angle_refined_deg 1.943 r_mcangle_it 1.498 r_mcbond_it 0.843 r_chiral_restr 0.127
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.927 r_dihedral_angle_3_deg 21.171 r_dihedral_angle_4_deg 19.553 r_dihedral_angle_1_deg 6.345 r_scangle_it 4.158 r_scbond_it 2.704 r_angle_refined_deg 1.943 r_mcangle_it 1.498 r_mcbond_it 0.843 r_chiral_restr 0.127 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9160 Nucleic Acid Atoms Solvent Atoms 274 Heterogen Atoms 256
Software Software Software Name Purpose HKL-2000 data collection MLPHARE phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling