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The 0.76 angstrom X-ray structure of the human heart fatty acid-binding protein complexed with petroselinic 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 7 293 0.1M Hepes-NaOH (pH7.0), 55% PEG 400
Crystal Properties Matthews coefficient Solvent content 2.16 43.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.726 α = 90 b = 69.613 β = 90 c = 33.62 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 MX300HE 2014-10-09 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) 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 0.76 50 99.6 0.1 7.3 11.5 157840
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 0.76 0.77 0.87 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 3WVM 0.76 22.13 149848 7902 99.37 0.12134 0.12105 0.1257 0.12708 0.1322 RANDOM 11.311
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 -0.12 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.078 r_rigid_bond_restr 19.511 r_dihedral_angle_1_deg 13.956 r_dihedral_angle_4_deg 13.533 r_dihedral_angle_3_deg 13.023 r_mcbond_other 10.058 r_mcbond_it 10.052 r_long_range_B_refined 9.115 r_long_range_B_other 7.47 r_mcangle_other 6.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.078 r_rigid_bond_restr 19.511 r_dihedral_angle_1_deg 13.956 r_dihedral_angle_4_deg 13.533 r_dihedral_angle_3_deg 13.023 r_mcbond_other 10.058 r_mcbond_it 10.052 r_long_range_B_refined 9.115 r_long_range_B_other 7.47 r_mcangle_other 6.306 r_mcangle_it 6.303 r_scangle_other 6.278 r_scbond_it 6.02 r_scbond_other 6.02 r_angle_refined_deg 1.949 r_angle_other_deg 1.576 r_chiral_restr 0.087 r_bond_refined_d 0.021 r_gen_planes_refined 0.012 r_bond_other_d 0.007 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 201 Heterogen Atoms 49
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing