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X-ray structure of high-strength hydrogel-grown FABP3 crystal soaked in 50% DMSO solution containing Indometacin
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), 50% PEG 400
Crystal Properties Matthews coefficient Solvent content 2.18 43.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.643 α = 90 b = 69.214 β = 90 c = 33.936 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 2015-05-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.800 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) 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 1.19 50 99.8 0.032 10.3 6.5 41963
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.19 1.21 0.306 2.3
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 1.19 30.49 39857 2130 99.78 0.15029 0.14826 0.1497 0.18902 0.1909 RANDOM 15.202
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] -0.38 -0.21 0.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.885 r_dihedral_angle_3_deg 14.047 r_dihedral_angle_4_deg 13.278 r_dihedral_angle_1_deg 6.848 r_rigid_bond_restr 3.652 r_long_range_B_refined 3.648 r_scangle_other 3.401 r_long_range_B_other 3.322 r_scbond_it 2.914 r_scbond_other 2.914
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.885 r_dihedral_angle_3_deg 14.047 r_dihedral_angle_4_deg 13.278 r_dihedral_angle_1_deg 6.848 r_rigid_bond_restr 3.652 r_long_range_B_refined 3.648 r_scangle_other 3.401 r_long_range_B_other 3.322 r_scbond_it 2.914 r_scbond_other 2.914 r_mcangle_it 2.08 r_mcangle_other 2.079 r_angle_refined_deg 2.038 r_mcbond_it 1.708 r_mcbond_other 1.566 r_angle_other_deg 1.55 r_chiral_restr 0.094 r_bond_refined_d 0.018 r_gen_planes_refined 0.011 r_bond_other_d 0.003 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 1036 Nucleic Acid Atoms Solvent Atoms 181 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing