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Crystal structure of the signaling protein complex 5
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 3.72 66.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 123.267 α = 90 b = 123.267 β = 90 c = 123.267 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 2015-05-17 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) 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 2.4 38.98 99.78 0.15 0.065 11.5 7.2 23398 71.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.49 100 2.54 7.2
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 MOLECULAR REPLACEMENT THROUGHOUT 4IAM 2.4 38.98 23398 1206 99.78 0.15038 0.14889 0.1495 0.17747 0.1711 RANDOM 93.567
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] -54.69 32.78 -23.6 -49.25 59.55 103.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.792 r_dihedral_angle_3_deg 16.236 r_dihedral_angle_4_deg 16.186 r_long_range_B_refined 8.138 r_long_range_B_other 8.137 r_scangle_other 6.214 r_dihedral_angle_1_deg 5.915 r_mcangle_other 5.423 r_mcangle_it 5.415 r_scbond_it 4.184
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.792 r_dihedral_angle_3_deg 16.236 r_dihedral_angle_4_deg 16.186 r_long_range_B_refined 8.138 r_long_range_B_other 8.137 r_scangle_other 6.214 r_dihedral_angle_1_deg 5.915 r_mcangle_other 5.423 r_mcangle_it 5.415 r_scbond_it 4.184 r_scbond_other 4.18 r_mcbond_it 3.911 r_mcbond_other 3.885 r_angle_refined_deg 1.314 r_angle_other_deg 0.91 r_chiral_restr 0.102 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_gen_planes_other 0.003 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 11 Heterogen Atoms 101
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing