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The 0.90 angstrom X-ray structure of the human heart fatty acid-binding protein complexed with heptanoic 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 8.5 293 0.1M Tris-HCl (pH8.5), 55% PEG 400
Crystal Properties Matthews coefficient Solvent content 2.18 43.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.588 α = 90 b = 69.815 β = 90 c = 33.896 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 2013-06-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.8000 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 0.9 43 93.1 0.061 12.4 9.6 90034
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 0.9 0.92 0.399 3.5
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 0.9 26.63 85357 4487 92.96 0.11358 0.11294 0.1204 0.12563 0.1345 RANDOM 9.718
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] 0.16 -0.13 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.409 r_dihedral_angle_4_deg 13.138 r_dihedral_angle_3_deg 11.796 r_rigid_bond_restr 11.263 r_dihedral_angle_1_deg 6.777 r_long_range_B_refined 5.353 r_long_range_B_other 4.577 r_mcbond_it 3.516 r_mcbond_other 3.516 r_mcangle_it 3.017
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.409 r_dihedral_angle_4_deg 13.138 r_dihedral_angle_3_deg 11.796 r_rigid_bond_restr 11.263 r_dihedral_angle_1_deg 6.777 r_long_range_B_refined 5.353 r_long_range_B_other 4.577 r_mcbond_it 3.516 r_mcbond_other 3.516 r_mcangle_it 3.017 r_mcangle_other 3.016 r_scangle_other 2.254 r_scbond_it 2.028 r_scbond_other 2.027 r_angle_refined_deg 1.89 r_angle_other_deg 1.576 r_chiral_restr 0.083 r_bond_refined_d 0.015 r_gen_planes_refined 0.01 r_bond_other_d 0.007 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 222 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing