☰ Navigation Tabs
Crystal structure of S. tokodaii Sua5 complexed with L-threonine and AMPPNP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2EQA PDB entry 2EQA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 303 0.1M acetate-Na buffer, 4.5M sodium nitrate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 303K
Crystal Properties Matthews coefficient Solvent content 2.26 45.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.35 α = 90 b = 121 β = 90 c = 68.01 γ = 90
Symmetry Space Group C 2 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 90 CCD ADSC QUANTUM 315 2008-05-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1 SPring-8 BL41XU
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 1.8 50 99.5 0.065 0.048 34.4 7.3 32711 22.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.86 98 0.567 0.503 2.5 6.2
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 PDB entry 2EQA 1.8 19.97 32691 32691 1623 99.3 0.198 0.198 0.1987 0.238 0.2361 RANDOM 29
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] -1.92 0.28 1.63
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.9 c_scangle_it 3.32 c_scbond_it 2.27 c_mcangle_it 1.93 c_angle_deg 1.7 c_improper_angle_d 1.33 c_mcbond_it 1.31 c_bond_d 0.011 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.9 c_scangle_it 3.32 c_scbond_it 2.27 c_mcangle_it 1.93 c_angle_deg 1.7 c_improper_angle_d 1.33 c_mcbond_it 1.31 c_bond_d 0.011 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2560 Nucleic Acid Atoms Solvent Atoms 291 Heterogen Atoms 63
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing CNS refinement HKL-2000 data reduction SCALEPACK data scaling