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Crystal structure of signalling protein from buffalo (SPB-40) with an acetone induced conformation of Trp78 at 1.49 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5WSI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.8 298 35mM Tris -HCl pH- 8.0, 25mM Nacl, 20% Acetone.
Crystal Properties Matthews coefficient Solvent content 2.62 52.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.457 α = 90 b = 66.517 β = 90 c = 105.847 γ = 90
Symmetry Space Group P 21 21 21
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 MARRESEARCH mirror 2014-10-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.97 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.49 56.32 99 0.03 11.4 4.2 65450 20.4
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 1.49 1.53 99 2.2
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 5WSI 1.49 56.32 65450 3479 98.47 0.14856 0.14707 0.1476 0.17641 0.1767 RANDOM 26.13
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] 1.29 -0.75 -0.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.158 r_dihedral_angle_4_deg 24.269 r_dihedral_angle_3_deg 13.297 r_dihedral_angle_1_deg 7.178 r_long_range_B_refined 4.811 r_long_range_B_other 4.811 r_scangle_other 3.723 r_angle_refined_deg 3.117 r_scbond_it 2.536 r_scbond_other 2.535
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.158 r_dihedral_angle_4_deg 24.269 r_dihedral_angle_3_deg 13.297 r_dihedral_angle_1_deg 7.178 r_long_range_B_refined 4.811 r_long_range_B_other 4.811 r_scangle_other 3.723 r_angle_refined_deg 3.117 r_scbond_it 2.536 r_scbond_other 2.535 r_mcangle_other 2.309 r_mcangle_it 2.307 r_angle_other_deg 1.84 r_mcbond_it 1.672 r_mcbond_other 1.667 r_chiral_restr 0.191 r_bond_refined_d 0.038 r_gen_planes_refined 0.017 r_bond_other_d 0.004 r_gen_planes_other 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 2877 Nucleic Acid Atoms Solvent Atoms 413 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing