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Crystal structure of the signaling protein complex 2
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,
Crystal Properties Matthews coefficient Solvent content 3.64 66.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.387 α = 90 b = 122.387 β = 90 c = 122.387 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 Mirror 2012-02-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-1 0.97945 SSRL BL9-1
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 2.3 38.7 99.24 0.12 0.1 14.6 6.2 25832
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 2.3 2.38 100 0.46 4.1 6.2
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 2.3 38.7 25832 1363 99.24 0.12587 0.12395 0.1401 0.16364 0.1706 RANDOM 50.697
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] -1.71 14.51 -14.91 0.78 -15.52 0.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.307 r_dihedral_angle_4_deg 21.913 r_dihedral_angle_3_deg 20.4 r_scangle_other 12.161 r_long_range_B_other 11.242 r_long_range_B_refined 11.227 r_scbond_it 10.254 r_scbond_other 10.247 r_mcangle_it 7.871 r_mcangle_other 7.869
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.307 r_dihedral_angle_4_deg 21.913 r_dihedral_angle_3_deg 20.4 r_scangle_other 12.161 r_long_range_B_other 11.242 r_long_range_B_refined 11.227 r_scbond_it 10.254 r_scbond_other 10.247 r_mcangle_it 7.871 r_mcangle_other 7.869 r_dihedral_angle_1_deg 7.18 r_mcbond_it 6.841 r_mcbond_other 6.825 r_angle_refined_deg 1.294 r_angle_other_deg 0.619 r_chiral_restr 0.12 r_gen_planes_refined 0.02 r_bond_refined_d 0.01 r_gen_planes_other 0.008 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 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 118 Heterogen Atoms 112
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing