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Structure of human amniotic fluid RBP4 saturated with palmitate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5NU6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 4.3 M NaCl, 100 mM Hepes, pH 7.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.84 α = 90 b = 102.84 β = 90 c = 73.164 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M-F 2016-02-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 1.0 ESRF ID29
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 1.5 56.53 93.8 0.042 9.7 2.1 43348
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 1.5 1.58 94.4 0.366 1.9 2.1
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 FOURIER SYNTHESIS THROUGHOUT 5NU6 1.5 30 41174 2150 93.73 0.17098 0.16969 0.197 0.19531 0.2087 RANDOM 37.771
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] 0.33 0.17 0.33 -1.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.905 r_sphericity_bonded 17.389 r_dihedral_angle_4_deg 16.783 r_sphericity_free 15.345 r_dihedral_angle_3_deg 14.232 r_rigid_bond_restr 12.527 r_scangle_other 9.121 r_scbond_it 8.561 r_scbond_other 8.558 r_dihedral_angle_1_deg 8.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.905 r_sphericity_bonded 17.389 r_dihedral_angle_4_deg 16.783 r_sphericity_free 15.345 r_dihedral_angle_3_deg 14.232 r_rigid_bond_restr 12.527 r_scangle_other 9.121 r_scbond_it 8.561 r_scbond_other 8.558 r_dihedral_angle_1_deg 8.4 r_long_range_B_other 7.832 r_long_range_B_refined 7.763 r_mcangle_it 6.798 r_mcangle_other 6.781 r_mcbond_other 6.758 r_mcbond_it 6.736 r_angle_other_deg 1.143 r_angle_refined_deg 0.769 r_chiral_restr 0.043 r_bond_other_d 0.006 r_bond_refined_d 0.004 r_gen_planes_refined 0.003 r_gen_planes_other 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1408 Nucleic Acid Atoms Solvent Atoms 102 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHENIX phasing