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X-ray structure of the human heart fatty acid-binding protein complexed with S-Ibuprofen
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 4.5 293 0.1M Na-citrate (pH4.5), 40% PEG 400
Crystal Properties Matthews coefficient Solvent content 3.05 59.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.524 α = 90 b = 107.866 β = 90 c = 48.195 γ = 90
Symmetry Space Group C 2 2 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 MARMOSAIC 225 mm CCD 2013-04-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.90000 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 1.5 50 99.7 0.064 9.5 8 29346
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 1.5 1.53 0.38 3.2
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 1.5 35.96 27842 1493 99.6 0.13995 0.13753 0.1404 0.18429 0.1855 RANDOM 25.027
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] 1.38 -0.87 -0.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.968 r_dihedral_angle_4_deg 16.057 r_dihedral_angle_3_deg 14.113 r_dihedral_angle_1_deg 6.835 r_rigid_bond_restr 6.668 r_long_range_B_refined 5.126 r_scangle_other 4.918 r_long_range_B_other 4.75 r_scbond_it 4.53 r_scbond_other 4.526
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.968 r_dihedral_angle_4_deg 16.057 r_dihedral_angle_3_deg 14.113 r_dihedral_angle_1_deg 6.835 r_rigid_bond_restr 6.668 r_long_range_B_refined 5.126 r_scangle_other 4.918 r_long_range_B_other 4.75 r_scbond_it 4.53 r_scbond_other 4.526 r_mcangle_other 3.376 r_mcangle_it 3.37 r_mcbond_it 3.053 r_mcbond_other 3.001 r_angle_refined_deg 2.116 r_angle_other_deg 1.758 r_chiral_restr 0.11 r_bond_refined_d 0.021 r_bond_other_d 0.018 r_gen_planes_refined 0.013 r_gen_planes_other 0.012 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 1039 Nucleic Acid Atoms Solvent Atoms 189 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing