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Structure of human urine RBP4 saturated with palmitate
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 3.57 65.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.79 α = 90 b = 102.79 β = 90 c = 73.634 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 1.59 56.74 90.9 0.053 9.2 2.5 35401
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 1.59 1.68 92.3 0.466 2 2.5
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 1.59 30 33661 1733 90.86 0.17203 0.16999 0.2034 0.21167 0.2179 RANDOM 45.439
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] 0.18 0.09 0.18 -0.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.515 r_sphericity_bonded 22.474 r_sphericity_free 18.729 r_dihedral_angle_4_deg 16.048 r_dihedral_angle_3_deg 14.933 r_rigid_bond_restr 13.296 r_long_range_B_other 12.423 r_long_range_B_refined 12.295 r_scangle_other 11.096 r_scbond_it 10.665
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.515 r_sphericity_bonded 22.474 r_sphericity_free 18.729 r_dihedral_angle_4_deg 16.048 r_dihedral_angle_3_deg 14.933 r_rigid_bond_restr 13.296 r_long_range_B_other 12.423 r_long_range_B_refined 12.295 r_scangle_other 11.096 r_scbond_it 10.665 r_scbond_other 10.658 r_mcangle_it 9.195 r_mcangle_other 9.195 r_mcbond_it 8.709 r_mcbond_other 8.703 r_dihedral_angle_1_deg 8.089 r_angle_other_deg 1.111 r_angle_refined_deg 0.643 r_chiral_restr 0.038 r_bond_other_d 0.006 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 113 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHENIX phasing