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The 1.05 angstrom X-ray structure of the human heart fatty acid-binding protein complexed with perfluorooctanoic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3WVM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 0.1M Tris-HCl (pH 8.0 or 8.5), 55% PEG 400
Crystal Properties Matthews coefficient Solvent content 2.14 42.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.689 α = 90 b = 68.819 β = 90 c = 33.752 γ = 90
Symmetry Space Group P 21 21 21
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 MX225HE 2014-11-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 0.90000 SPring-8 BL38B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 1.05 50 96.1 0.045 0.013 13.5 11.7 57949
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.05 1.07 0.343 0.115 4.4
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 3WVM 1.05 15.71 54990 2925 96.12 0.11817 0.11715 0.1216 0.1376 0.1418 RANDOM 14.286
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] -0.21 0.31 -0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.209 r_dihedral_angle_4_deg 14.725 r_dihedral_angle_3_deg 14.401 r_rigid_bond_restr 11.494 r_scbond_it 9.912 r_scbond_other 9.907 r_long_range_B_refined 7.625 r_long_range_B_other 7.588 r_scangle_other 7.237 r_dihedral_angle_1_deg 6.831
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.209 r_dihedral_angle_4_deg 14.725 r_dihedral_angle_3_deg 14.401 r_rigid_bond_restr 11.494 r_scbond_it 9.912 r_scbond_other 9.907 r_long_range_B_refined 7.625 r_long_range_B_other 7.588 r_scangle_other 7.237 r_dihedral_angle_1_deg 6.831 r_mcangle_it 2.683 r_mcangle_other 2.682 r_mcbond_it 2.375 r_mcbond_other 2.369 r_angle_refined_deg 2.329 r_angle_other_deg 1.647 r_chiral_restr 0.123 r_bond_refined_d 0.022 r_gen_planes_refined 0.012 r_bond_other_d 0.01 r_gen_planes_other 0.005 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1041 Nucleic Acid Atoms Solvent Atoms 203 Heterogen Atoms 70
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing