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The 0.87 angstrom X-ray structure of the human heart fatty acid-binding protein complexed with nonadecanoic 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 (pH8.0), 55% PEG 400
Crystal Properties Matthews coefficient Solvent content 2.18 43.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.609 α = 90 b = 69.762 β = 90 c = 33.908 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 2013-05-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.8000 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 0.87 43 98.1 0.058 11.2 12.4 105027
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 0.87 0.89 0.403 4.9
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 0.87 28.82 99540 5228 97.76 0.10448 0.10416 0.1046 0.11072 0.1112 RANDOM 10.021
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] 0.05 -0.04 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.488 r_rigid_bond_restr 17.829 r_dihedral_angle_4_deg 14.136 r_dihedral_angle_3_deg 11.107 r_long_range_B_refined 8.774 r_scbond_it 8.608 r_scbond_other 8.602 r_long_range_B_other 8.491 r_scangle_other 6.973 r_dihedral_angle_1_deg 6.431
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.488 r_rigid_bond_restr 17.829 r_dihedral_angle_4_deg 14.136 r_dihedral_angle_3_deg 11.107 r_long_range_B_refined 8.774 r_scbond_it 8.608 r_scbond_other 8.602 r_long_range_B_other 8.491 r_scangle_other 6.973 r_dihedral_angle_1_deg 6.431 r_mcangle_it 5.042 r_mcangle_other 5.041 r_mcbond_it 4.839 r_mcbond_other 4.838 r_angle_refined_deg 2.165 r_angle_other_deg 1.69 r_chiral_restr 0.098 r_bond_refined_d 0.021 r_bond_other_d 0.018 r_gen_planes_refined 0.011 r_gen_planes_other 0.004 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 219 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing