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X-ray structure of high-strength hydrogel-grown FABP3 crystal soaked in 50% DMSO solution containing dibutylhydroxytoluene (BHT)
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 8 294 0.1M Tris-HCl (pH8.0), 50% PEG 400
Crystal Properties Matthews coefficient Solvent content 2.19 43.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.774 α = 90 b = 70.219 β = 90 c = 33.776 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 2012-06-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 0.97884 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 1 50 99.8 0.053 10.4 7 71177
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 1.02 0.5 1.7
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 28.77 67351 3583 99.59 0.11417 0.11348 0.1165 0.12691 0.1295 RANDOM 12.668
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] 0.15 -0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.352 r_rigid_bond_restr 22.76 r_dihedral_angle_4_deg 14.622 r_dihedral_angle_3_deg 14.248 r_dihedral_angle_1_deg 6.522 r_scbond_it 6.243 r_scbond_other 6.238 r_long_range_B_refined 5.684 r_long_range_B_other 5.51 r_scangle_other 4.899
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.352 r_rigid_bond_restr 22.76 r_dihedral_angle_4_deg 14.622 r_dihedral_angle_3_deg 14.248 r_dihedral_angle_1_deg 6.522 r_scbond_it 6.243 r_scbond_other 6.238 r_long_range_B_refined 5.684 r_long_range_B_other 5.51 r_scangle_other 4.899 r_mcangle_other 3.101 r_mcangle_it 2.982 r_mcbond_it 2.817 r_mcbond_other 2.37 r_angle_refined_deg 2.187 r_angle_other_deg 1.565 r_chiral_restr 0.11 r_bond_refined_d 0.019 r_gen_planes_refined 0.013 r_gen_planes_other 0.006 r_bond_other_d 0.005 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 300 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing