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The 1.00 angstrom X-ray structure of the human heart fatty acid-binding protein complexed with perfluoroheptanoic 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 2.18 43.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.829 α = 90 b = 69.493 β = 90 c = 33.881 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 2014-10-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 0.80000 SPring-8 BL38B1
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 1 50 96.3 0.085 14.3 4.6 68057
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 1 1.02 0.279 2.1
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 28.84 64502 3451 96.07 0.12335 0.12203 0.1244 0.147 0.1495 RANDOM 14.601
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] -0.63 1.11 -0.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.695 r_dihedral_angle_4_deg 15.275 r_rigid_bond_restr 12.497 r_dihedral_angle_3_deg 12.361 r_dihedral_angle_1_deg 6.961 r_scangle_other 6.769 r_long_range_B_refined 5.979 r_scbond_it 5.846 r_scbond_other 5.846 r_long_range_B_other 5.263
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.695 r_dihedral_angle_4_deg 15.275 r_rigid_bond_restr 12.497 r_dihedral_angle_3_deg 12.361 r_dihedral_angle_1_deg 6.961 r_scangle_other 6.769 r_long_range_B_refined 5.979 r_scbond_it 5.846 r_scbond_other 5.846 r_long_range_B_other 5.263 r_mcangle_other 3.073 r_mcbond_it 2.787 r_mcangle_it 2.773 r_angle_refined_deg 2.337 r_mcbond_other 1.864 r_angle_other_deg 1.57 r_chiral_restr 0.109 r_bond_refined_d 0.023 r_gen_planes_refined 0.012 r_bond_other_d 0.005 r_gen_planes_other 0.003 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 220 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing