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Crystal structure of signaling protein SPB-40 complexed with 5-hydroxymethyl oxalanetriol at 2.80 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 VAPOR DIFFUSION, HANGING DROP 8 298 25mM Tris, 50mM NaCl, 20% ethanol, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.65 53.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.809 α = 90 b = 66.943 β = 90 c = 106.54 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 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 2.79 50 100 0.108 16.6 11280 11280
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 2.8 2.85 100 0.46 4.1
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 (All) 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 2.79 41.72 11280 10703 535 99.56 0.18241 0.18239 0.18192 0.1918 0.23391 0.253 RANDOM 32.923
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] -0.74 -1.17 1.91
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.309 r_dihedral_angle_3_deg 21.274 r_dihedral_angle_4_deg 20.704 r_long_range_B_refined 7.658 r_long_range_B_other 7.657 r_dihedral_angle_1_deg 7 r_scangle_other 4.146 r_mcangle_other 3.828 r_mcangle_it 3.824 r_scbond_it 2.464
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.309 r_dihedral_angle_3_deg 21.274 r_dihedral_angle_4_deg 20.704 r_long_range_B_refined 7.658 r_long_range_B_other 7.657 r_dihedral_angle_1_deg 7 r_scangle_other 4.146 r_mcangle_other 3.828 r_mcangle_it 3.824 r_scbond_it 2.464 r_scbond_other 2.463 r_mcbond_it 2.227 r_mcbond_other 2.216 r_angle_refined_deg 1.861 r_angle_other_deg 0.849 r_chiral_restr 0.086 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2894 Nucleic Acid Atoms Solvent Atoms 110 Heterogen Atoms 30
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling