☰ Navigation Tabs
Crystal structure of butanol modified signaling protein from buffalo (SPB-40) at 1.65 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5YAR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 298 35mM Tris-HCl, 25mM NaCl, 20% ethanol, pH 8.0
Crystal Properties Matthews coefficient Solvent content 2.7 54.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.142 α = 90 b = 66.553 β = 90 c = 106.005 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 2014-11-13 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 1.65 56.37 100 0.052 5.8 5.4 52856
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 1.65 1.69 100 0.309 5.8 5.2
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 5YAR 1.65 56.37 50253 2543 99.2 0.1669 0.16495 0.1776 0.20582 0.212 RANDOM 28.446
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] 0.26 -0.4 0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.2 r_dihedral_angle_4_deg 21.58 r_dihedral_angle_3_deg 14.128 r_long_range_B_refined 7.686 r_long_range_B_other 7.686 r_dihedral_angle_1_deg 6.32 r_scangle_other 6.023 r_scbond_it 4.063 r_scbond_other 4.061 r_mcangle_other 3.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.2 r_dihedral_angle_4_deg 21.58 r_dihedral_angle_3_deg 14.128 r_long_range_B_refined 7.686 r_long_range_B_other 7.686 r_dihedral_angle_1_deg 6.32 r_scangle_other 6.023 r_scbond_it 4.063 r_scbond_other 4.061 r_mcangle_other 3.85 r_mcangle_it 3.843 r_mcbond_it 2.909 r_mcbond_other 2.909 r_angle_refined_deg 2.34 r_angle_other_deg 1.203 r_chiral_restr 0.153 r_bond_refined_d 0.026 r_gen_planes_refined 0.012 r_bond_other_d 0.002 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 2874 Nucleic Acid Atoms Solvent Atoms 394 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing