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X-ray structure of iFABP from human and rat with bound fluorescent fatty acid analogue
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2IFB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 277 30-45% w/v PEG 2000, 0.1M Tris pH 7.0, 0.2M magnesium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.08 40.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.59 α = 90 b = 50.59 β = 90 c = 97.452 γ = 90
Symmetry Space Group P 43 21 2
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 210r Mirrors 2008-04-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 0.954 Australian Synchrotron MX1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.6 44.9 100 0.056 0.057 42 27.7 17480 17480 2 20.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.69 100 0.382 0.389 10.1 28.1 2499
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2IFB 1.6 44.9 2 16540 16540 880 99.99 0.22642 0.22483 0.25671 0.2684 RANDOM 19.348
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] 0.01 0.01 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.415 r_dihedral_angle_4_deg 17.712 r_dihedral_angle_3_deg 12.233 r_dihedral_angle_1_deg 6.071 r_scangle_it 3.834 r_scbond_it 2.456 r_mcangle_it 1.615 r_angle_refined_deg 1.377 r_mcbond_it 0.96 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.415 r_dihedral_angle_4_deg 17.712 r_dihedral_angle_3_deg 12.233 r_dihedral_angle_1_deg 6.071 r_scangle_it 3.834 r_scbond_it 2.456 r_mcangle_it 1.615 r_angle_refined_deg 1.377 r_mcbond_it 0.96 r_nbtor_refined 0.308 r_nbd_refined 0.193 r_symmetry_vdw_refined 0.157 r_symmetry_hbond_refined 0.13 r_xyhbond_nbd_refined 0.11 r_chiral_restr 0.096 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1047 Nucleic Acid Atoms Solvent Atoms 50 Heterogen Atoms 30
Software Software Software Name Purpose Blu-Ice data collection AMoRE phasing REFMAC refinement MOSFLM data reduction SCALA data scaling