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Structure of human urine RBP4 saturated with laurate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5NU2
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 3.55 65.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.82 α = 90 b = 102.82 β = 90 c = 73.274 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 56.58 99.1 0.048 13.2 4.5 37778
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 98.5 0.444 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 5NU2 1.6 56.58 35785 1967 99.07 0.17131 0.16992 0.2099 0.19668 0.2144 RANDOM 44.668
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] 0.22 0.11 0.22 -0.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.745 r_sphericity_bonded 29.147 r_dihedral_angle_4_deg 23.944 r_sphericity_free 21.533 r_rigid_bond_restr 15.617 r_dihedral_angle_3_deg 15.361 r_long_range_B_other 13.287 r_long_range_B_refined 13.173 r_scangle_other 12.883 r_scbond_other 12.632
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.745 r_sphericity_bonded 29.147 r_dihedral_angle_4_deg 23.944 r_sphericity_free 21.533 r_rigid_bond_restr 15.617 r_dihedral_angle_3_deg 15.361 r_long_range_B_other 13.287 r_long_range_B_refined 13.173 r_scangle_other 12.883 r_scbond_other 12.632 r_scbond_it 12.624 r_mcangle_it 10.618 r_mcangle_other 10.562 r_mcbond_it 10.237 r_mcbond_other 10.235 r_dihedral_angle_1_deg 8.986 r_angle_other_deg 0.987 r_angle_refined_deg 0.618 r_chiral_restr 0.04 r_bond_other_d 0.005 r_bond_refined_d 0.003 r_gen_planes_refined 0.002 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 110 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling