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Crystal structure of the complex of buffalo signaling protein SPB-40 with N-acetylglucosamine at 2.65 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2O9O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 298 25mM Tris, 50mM NaCl, 20% ethanol, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.67 53.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.938 α = 90 b = 67.11 β = 90 c = 107.006 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 77 CCD MARRESEARCH MIRROR 2013-07-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 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 2.65 50 100 0.102 17.8 13282
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.65 2.7 100 0.433 4.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 2O9O 2.65 41.61 13282 12604 655 99.8 0.177 0.174 0.1792 0.234 0.2478 RANDOM 25.78
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] -0.47 -1.09 1.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.41 r_dihedral_angle_4_deg 23.86 r_dihedral_angle_3_deg 21.446 r_long_range_B_refined 7.256 r_long_range_B_other 7.232 r_dihedral_angle_1_deg 6.998 r_scangle_other 4.318 r_mcangle_other 3.672 r_mcangle_it 3.665 r_scbond_it 2.557
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.41 r_dihedral_angle_4_deg 23.86 r_dihedral_angle_3_deg 21.446 r_long_range_B_refined 7.256 r_long_range_B_other 7.232 r_dihedral_angle_1_deg 6.998 r_scangle_other 4.318 r_mcangle_other 3.672 r_mcangle_it 3.665 r_scbond_it 2.557 r_scbond_other 2.556 r_mcbond_it 2.131 r_mcbond_other 2.095 r_angle_refined_deg 1.807 r_angle_other_deg 0.947 r_chiral_restr 0.097 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_bond_other_d 0.003 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 2894 Nucleic Acid Atoms Solvent Atoms 140 Heterogen Atoms 35
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling