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Structure of mutant tryptophan synthase alpha-subunit (D110A) from a hyperthermophile, Pyrococcus furiosus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GEQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 283 0.1M MES-NAOH, 10-15% PEG 20000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 283K
Crystal Properties Matthews coefficient Solvent content 2.15 42.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.116 α = 90 b = 77.645 β = 90 c = 166.543 γ = 90
Symmetry Space Group C 2 2 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 MAR CCD 165 mm mirror 2001-05-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0 SPring-8 BL41XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.2 50 93.2 0.036 46.6 5.27 22853 22853 30.6
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) 2.2 2.28 73.7 0.123 11.7 5.27 1788
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 1GEQ 2.4 19.94 18572 18472 907 97.7 0.182 0.182 0.264 RANDOM 27
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] -1.53 1.3 0.22
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21.8 c_scangle_it 4.58 c_scbond_it 3.29 c_mcangle_it 2.97 c_mcbond_it 2.04 c_angle_deg 1.4 c_improper_angle_d 0.76 c_bond_d 0.008 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21.8 c_scangle_it 4.58 c_scbond_it 3.29 c_mcangle_it 2.97 c_mcbond_it 2.04 c_angle_deg 1.4 c_improper_angle_d 0.76 c_bond_d 0.008 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 3831 Nucleic Acid Atoms Solvent Atoms 628 Heterogen Atoms
Software Software Software Name Purpose CNS refinement MAR345dtb data collection HKL-2000 data reduction HKL-2000 data scaling CNS phasing