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Structure of non-fluorescent human urine RBP4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5NTY
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 = 102.68 α = 90 b = 102.68 β = 90 c = 73.18 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 2015-11-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 1.0 ESRF ID23-1
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 56.49 96.7 0.037 10.5 2.4 44537
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 96.3 0.443 1.8 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 FOURIER SYNTHESIS THROUGHOUT 5NTY 1.5 30 43086 2267 98.4 0.15783 0.15648 0.1935 0.18362 0.2078 RANDOM 41.007
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] 0.62 0.31 0.62 -2.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.701 r_sphericity_bonded 28.189 r_sphericity_free 20.401 r_rigid_bond_restr 17.629 r_dihedral_angle_4_deg 17.514 r_dihedral_angle_3_deg 14.917 r_long_range_B_other 14.866 r_long_range_B_refined 14.689 r_scangle_other 13.973 r_scbond_it 13.436
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.701 r_sphericity_bonded 28.189 r_sphericity_free 20.401 r_rigid_bond_restr 17.629 r_dihedral_angle_4_deg 17.514 r_dihedral_angle_3_deg 14.917 r_long_range_B_other 14.866 r_long_range_B_refined 14.689 r_scangle_other 13.973 r_scbond_it 13.436 r_scbond_other 13.429 r_mcbond_it 10.736 r_mcbond_other 10.73 r_mcangle_other 10.523 r_mcangle_it 10.502 r_dihedral_angle_1_deg 8.54 r_angle_other_deg 1.087 r_angle_refined_deg 0.702 r_chiral_restr 0.041 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 124 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHENIX phasing