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The 0.90 angstrom X-ray structure of the human heart fatty acid-binding protein complexed with trans-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 6.5 277 0.1M Mes-NaOH (pH6.5), 55% PEG 400
Crystal Properties Matthews coefficient Solvent content 2.13 42.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.511 α = 90 b = 69.365 β = 90 c = 33.45 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 0.9 50 99.5 0.032 8.6 8.8 94324
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 0.9 0.92 99.7 0.23 2.2 6.9
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 26.38 89628 4637 99.51 0.11525 0.11464 0.1146 0.12731 0.1272 RANDOM 10.928
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] -0.35 0.17 0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.588 r_dihedral_angle_4_deg 15.173 r_dihedral_angle_3_deg 13.293 r_rigid_bond_restr 9.384 r_dihedral_angle_1_deg 6.16 r_scbond_it 3.89 r_scbond_other 3.89 r_long_range_B_refined 3.802 r_scangle_other 3.774 r_long_range_B_other 3.442
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.588 r_dihedral_angle_4_deg 15.173 r_dihedral_angle_3_deg 13.293 r_rigid_bond_restr 9.384 r_dihedral_angle_1_deg 6.16 r_scbond_it 3.89 r_scbond_other 3.89 r_long_range_B_refined 3.802 r_scangle_other 3.774 r_long_range_B_other 3.442 r_angle_refined_deg 1.997 r_mcangle_it 1.623 r_mcangle_other 1.623 r_angle_other_deg 1.549 r_mcbond_it 1.269 r_mcbond_other 1.245 r_chiral_restr 0.104 r_bond_refined_d 0.02 r_gen_planes_refined 0.011 r_bond_other_d 0.004 r_gen_planes_other 0.002 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 173 Heterogen Atoms 55
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing