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X-ray structure of human heart fatty acid-binding protein delipidated with Lipidex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4TKJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 0.1M Tris-HCl (pH8.5), 50% PEG 400
Crystal Properties Matthews coefficient Solvent content 2.17 43.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.559 α = 90 b = 69.915 β = 90 c = 33.893 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 ADSC QUANTUM 315 2012-04-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 0.900 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 0.8 43.01 94.2 0.073 14.9 6.9 129294
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 0.8 0.81 0.429 2.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 0.8 22.23 122701 6505 94.12 0.13813 0.13776 0.1463 0.14511 0.1543 RANDOM 16.849
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] -0.3 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.583 r_long_range_B_other 19.851 r_long_range_B_refined 19.638 r_mcangle_it 15.999 r_mcangle_other 15.992 r_dihedral_angle_4_deg 13.781 r_rigid_bond_restr 13.526 r_scangle_other 13.36 r_mcbond_other 12.238 r_mcbond_it 12.234
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.583 r_long_range_B_other 19.851 r_long_range_B_refined 19.638 r_mcangle_it 15.999 r_mcangle_other 15.992 r_dihedral_angle_4_deg 13.781 r_rigid_bond_restr 13.526 r_scangle_other 13.36 r_mcbond_other 12.238 r_mcbond_it 12.234 r_dihedral_angle_3_deg 12.128 r_scbond_it 11.815 r_scbond_other 11.806 r_dihedral_angle_1_deg 6.595 r_angle_refined_deg 1.754 r_angle_other_deg 1.544 r_chiral_restr 0.07 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_bond_other_d 0.004 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 1044 Nucleic Acid Atoms Solvent Atoms 197 Heterogen Atoms 19
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing