☰ Navigation Tabs
Crystal structure of the signaling protein complex 4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4IAM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 295 1.9M sodium malonate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 3.63 66.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.349 α = 90 b = 122.349 β = 90 c = 122.349 γ = 90
Symmetry Space Group P 21 3
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 325 mm CCD Mirrors 2014-08-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL7-1 0.97945 SSRL BL7-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) CC (Half) 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 2.35 38.69 99.82 0.16 0.085 0.955 12.2 7.3 24332 49.9
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 2.35 2.43 100 0.23 9.7 7.4
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4IAM 2.35 38.69 24322 1332 99.82 0.11896 0.11632 0.16906 0.2266 RANDOM 49.909
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] -9.69 -3.3 2.77 6.78 -20.66 2.92
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.214 r_dihedral_angle_4_deg 18.809 r_dihedral_angle_3_deg 17.995 r_long_range_B_other 11.55 r_long_range_B_refined 11.542 r_scangle_other 11.203 r_scbond_other 8.416 r_scbond_it 8.415 r_mcangle_other 7.922 r_mcangle_it 7.919
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.214 r_dihedral_angle_4_deg 18.809 r_dihedral_angle_3_deg 17.995 r_long_range_B_other 11.55 r_long_range_B_refined 11.542 r_scangle_other 11.203 r_scbond_other 8.416 r_scbond_it 8.415 r_mcangle_other 7.922 r_mcangle_it 7.919 r_dihedral_angle_1_deg 6.668 r_mcbond_it 6.355 r_mcbond_other 6.339 r_angle_refined_deg 2.925 r_angle_other_deg 1.658 r_chiral_restr 0.177 r_gen_planes_refined 0.014 r_bond_refined_d 0.011 r_gen_planes_other 0.007 r_bond_other_d 0.002 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2864 Nucleic Acid Atoms Solvent Atoms 90 Heterogen Atoms 109
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing