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The 0.95 angstrom X-ray structure of the human heart fatty acid-binding protein complexed with hexanoic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3FR2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 0.1M Mes-NaOH (pH6.5), 55% PEG 400
Crystal Properties Matthews coefficient Solvent content 2.18 43.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.674 α = 90 b = 69.924 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 PIXEL DECTRIS EIGER X 16M 2021-10-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.800 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 0.95 43.07 99.9 0.045 0.028 0.998 23.6 6.5 82207
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 0.95 0.97 0.233 0.146 0.973 6.2
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 3FR2 0.95 43.07 78001 4147 99.82 0.11965 0.11912 0.1218 0.12963 0.1298 RANDOM 10.411
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] -0.18 0.04 0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.162 r_dihedral_angle_4_deg 15.381 r_dihedral_angle_3_deg 11.749 r_rigid_bond_restr 10.512 r_dihedral_angle_1_deg 6.328 r_scbond_it 5.702 r_scbond_other 5.702 r_scangle_other 5.684 r_long_range_B_refined 4.582 r_long_range_B_other 4.112
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.162 r_dihedral_angle_4_deg 15.381 r_dihedral_angle_3_deg 11.749 r_rigid_bond_restr 10.512 r_dihedral_angle_1_deg 6.328 r_scbond_it 5.702 r_scbond_other 5.702 r_scangle_other 5.684 r_long_range_B_refined 4.582 r_long_range_B_other 4.112 r_mcbond_other 2.394 r_mcbond_it 2.39 r_mcangle_other 2.38 r_mcangle_it 2.379 r_angle_refined_deg 2.255 r_angle_other_deg 1.71 r_chiral_restr 0.102 r_bond_refined_d 0.021 r_bond_other_d 0.02 r_gen_planes_refined 0.012 r_gen_planes_other 0.004 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 235 Heterogen Atoms 21
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing