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The 0.83 angstrom X-ray structure of the human heart fatty acid-binding protein complexed with cis-vaccenic 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 6.5 293 0.1M Mes-NaOH (pH6.5), 45% PEG 400
Crystal Properties Matthews coefficient Solvent content 2.16 43.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.656 α = 90 b = 69.73 β = 90 c = 33.621 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 2014-12-14 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) 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 0.83 50 95.7 0.03 9.9 9.2 116840
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 0.83 0.84 0.251 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 0.83 28.65 111032 5766 95.61 0.12123 0.1208 0.1285 0.12966 0.1362 RANDOM 10.17
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] -0.26 0.21 0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.218 r_dihedral_angle_4_deg 15.937 r_dihedral_angle_3_deg 13.026 r_rigid_bond_restr 9.906 r_dihedral_angle_1_deg 6.166 r_long_range_B_refined 3.94 r_long_range_B_other 3.481 r_scangle_other 2.927 r_scbond_it 2.649 r_scbond_other 2.649
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.218 r_dihedral_angle_4_deg 15.937 r_dihedral_angle_3_deg 13.026 r_rigid_bond_restr 9.906 r_dihedral_angle_1_deg 6.166 r_long_range_B_refined 3.94 r_long_range_B_other 3.481 r_scangle_other 2.927 r_scbond_it 2.649 r_scbond_other 2.649 r_angle_refined_deg 2.57 r_angle_other_deg 1.818 r_mcangle_it 1.633 r_mcangle_other 1.633 r_mcbond_it 1.381 r_mcbond_other 1.271 r_chiral_restr 0.108 r_bond_refined_d 0.024 r_bond_other_d 0.017 r_gen_planes_refined 0.013 r_gen_planes_other 0.007 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 212 Heterogen Atoms 71
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing