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Structure of human holo plasma RBP4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BRP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICRODIALYSIS 277 4.5 M NaCl, 20 mM Na cacodylate, pH 6.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.097 α = 90 b = 103.097 β = 90 c = 73.552 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 2015-03-14 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 38.16 99.5 0.058 12.6 4.3 46674
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 99.4 0.462 2.8
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 MOLECULAR REPLACEMENT THROUGHOUT 1BRP 1.5 30 44136 2287 99.46 0.18114 0.17973 0.2071 0.2096 0.2195 RANDOM 41.232
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] 0.57 0.29 0.57 -1.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.606 r_sphericity_bonded 23.057 r_sphericity_free 17.405 r_rigid_bond_restr 16.335 r_scangle_other 15.074 r_dihedral_angle_4_deg 14.859 r_long_range_B_other 14.317 r_long_range_B_refined 14.239 r_scbond_it 14.122 r_scbond_other 14.113
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.606 r_sphericity_bonded 23.057 r_sphericity_free 17.405 r_rigid_bond_restr 16.335 r_scangle_other 15.074 r_dihedral_angle_4_deg 14.859 r_long_range_B_other 14.317 r_long_range_B_refined 14.239 r_scbond_it 14.122 r_scbond_other 14.113 r_dihedral_angle_3_deg 12.794 r_mcangle_it 9.084 r_mcangle_other 9.084 r_dihedral_angle_1_deg 8.896 r_mcbond_other 8.302 r_mcbond_it 8.3 r_angle_refined_deg 0.641 r_angle_other_deg 0.462 r_chiral_restr 0.04 r_gen_planes_other 0.005 r_gen_planes_refined 0.004 r_bond_refined_d 0.003 r_bond_other_d 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 77 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling