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PHENYLALANYL TRNA SYNTHETASE COMPLEXED WITH PHENYLALANINYL-ADENYLATE
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PYS PDB ENTRY 1PYS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 313 HANGING-DROP TECHNIQUE AT 4O C WITH (NH4)2SO4 AS PRECIPITANT. EACH DROPLET OF THE PHENYLALANYL-TRNA SYNTHETASE SOLUTION (10 microliters) AT PROTEIN CONCENTRATION OF 3 TO 5 MG PER ML IN 20 MM IMIDASOL-HCL BUFFER (PH 7.8), 1 MM MGCL2, 1 MM NAN3 AND 15% SATURATED (NH4)2SO4 IN THE SAME BUFFER. CRYSTALS APPEARED AFTER ONE TO TWO WEEKS AND GREW UP TO THE MAXIMAL DIMENSIONS OF 0.4X0.4X0.25 MM IN A FEW WEEKS, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 313K
Crystal Properties Matthews coefficient Solvent content 3.8 70
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 174.5 α = 90 b = 174.5 β = 90 c = 140.2 γ = 120
Symmetry Space Group P 32 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 IMAGE PLATE RIGAKU 1998-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 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 2.5 50 95.7 0.064 6 4 81613 81613 45
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) 1 2.5 2.59 88.5 0.399 2.2 4
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-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 1PYS 2.5 50 81613 81613 4000 95.7 0.23 0.2285 0.267 0.264 RANDOM 62
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]
RMS Deviations Key Refinement Restraint Deviation x_dihedral_angle_d 25 x_scangle_it 8.5 x_scbond_it 6 x_mcangle_it 5.2 x_mcbond_it 3.7 x_angle_deg 1.72 x_improper_angle_d 0.83 x_bond_d 0.01 x_bond_d_na x_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation x_dihedral_angle_d 25 x_scangle_it 8.5 x_scbond_it 6 x_mcangle_it 5.2 x_mcbond_it 3.7 x_angle_deg 1.72 x_improper_angle_d 0.83 x_bond_d 0.01 x_bond_d_na x_bond_d_prot x_angle_d x_angle_d_na x_angle_d_prot x_angle_deg_na x_angle_deg_prot x_dihedral_angle_d_na x_dihedral_angle_d_prot x_improper_angle_d_na x_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8166 Nucleic Acid Atoms Solvent Atoms 239 Heterogen Atoms 34
Software Software Software Name Purpose X-PLOR model building X-PLOR refinement DENZO data reduction SCALEPACK data scaling X-PLOR phasing