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Structure of human amniotic fluid RBP4 saturated with laurate
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 Properties Matthews coefficient Solvent content 3.53 65.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.61 α = 90 b = 102.61 β = 90 c = 73.134 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 1.6 56.47 99.3 0.054 12.8 4.6 37622
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 1.6 1.69 98.7 0.481 2.6 4.2
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 1.6 30 35652 1953 99.24 0.1752 0.17355 0.1997 0.20495 0.2133 RANDOM 40.874
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] 1.06 0.53 1.06 -3.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.064 r_sphericity_bonded 17.833 r_dihedral_angle_4_deg 16.347 r_sphericity_free 15.48 r_dihedral_angle_3_deg 14.206 r_rigid_bond_restr 13.59 r_dihedral_angle_1_deg 8.589 r_long_range_B_other 7.921 r_long_range_B_refined 7.832 r_scbond_it 7.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.064 r_sphericity_bonded 17.833 r_dihedral_angle_4_deg 16.347 r_sphericity_free 15.48 r_dihedral_angle_3_deg 14.206 r_rigid_bond_restr 13.59 r_dihedral_angle_1_deg 8.589 r_long_range_B_other 7.921 r_long_range_B_refined 7.832 r_scbond_it 7.66 r_scbond_other 7.655 r_scangle_other 7.588 r_mcangle_it 6.782 r_mcangle_other 6.774 r_mcbond_it 6.065 r_mcbond_other 6.06 r_angle_other_deg 0.982 r_angle_refined_deg 0.678 r_chiral_restr 0.042 r_bond_other_d 0.005 r_bond_refined_d 0.003 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 109 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHENIX phasing