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The 0.95 angstrom X-ray structure of the human heart fatty acid-binding protein complexed with undecanoic 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 9 293 0.1M Glycin-NaOH (pH9.0), 55% PEG 400
Crystal Properties Matthews coefficient Solvent content 2.16 43.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.657 α = 90 b = 69.908 β = 90 c = 33.71 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 BL38B1 0.9000 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 0.95 43.05 99.1 0.06 7 12.5 81542
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 0.95 0.97 0.372 2.6
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 0.95 24.28 77391 4089 99.02 0.10405 0.10356 0.1039 0.11316 0.1144 RANDOM 10.831
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] 0.1 -0.06 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.528 r_dihedral_angle_4_deg 14.891 r_dihedral_angle_3_deg 14.297 r_rigid_bond_restr 6.212 r_dihedral_angle_1_deg 6.176 r_long_range_B_refined 5.459 r_scangle_other 4.864 r_long_range_B_other 4.712 r_scbond_other 4.398 r_scbond_it 4.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.528 r_dihedral_angle_4_deg 14.891 r_dihedral_angle_3_deg 14.297 r_rigid_bond_restr 6.212 r_dihedral_angle_1_deg 6.176 r_long_range_B_refined 5.459 r_scangle_other 4.864 r_long_range_B_other 4.712 r_scbond_other 4.398 r_scbond_it 4.34 r_angle_other_deg 2.094 r_angle_refined_deg 2.013 r_mcangle_other 1.686 r_mcangle_it 1.685 r_mcbond_it 1.286 r_mcbond_other 1.273 r_chiral_restr 0.097 r_bond_refined_d 0.021 r_bond_other_d 0.021 r_gen_planes_refined 0.014 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 208 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing