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Crystal structure of selenophosphate synthetase from Aquifex aeolicus complexed with AMPCPP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YYD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.4 293 17% PEG8000, 50mM KH2PO4, 0.1M MES, 1mM AMPCPP, 5mM CoCl2, pH 6.4, VAPOR DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.99 38.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.536 α = 90 b = 80.536 β = 90 c = 160.641 γ = 120
Symmetry Space Group P 31 2 1
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 ADSC QUANTUM 315 monochromater 2006-03-27 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 2.1 50 99.9 0.108 0.108 19.6 6 36487 18.8
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 2.1 2.18 100 0.682 0.682 3 6 3592
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 2YYD 2.1 42.47 35947 1783 99.9 0.173 0.173 0.1764 0.225 0.1717 RANDOM 35.7
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] 0.54 -0.24 0.54 -1.08
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23 c_scangle_it 8.3 c_scbond_it 6.15 c_mcangle_it 4.88 c_mcbond_it 3.79 c_angle_deg 1.4 c_improper_angle_d 0.85 c_bond_d 0.009 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23 c_scangle_it 8.3 c_scbond_it 6.15 c_mcangle_it 4.88 c_mcbond_it 3.79 c_angle_deg 1.4 c_improper_angle_d 0.85 c_bond_d 0.009 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 5246 Nucleic Acid Atoms Solvent Atoms 279 Heterogen Atoms 77
Software Software Software Name Purpose CNS refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing