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Giardia lamblia Prolyl-tRNA synthetase in complex with prolyl-adenylate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NJ5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 sitting drop vapor diffusion 7.8 298 28% PEG 3350, 0.21 M MgCl2, 0.1 M Tris-HCl (pH 7.8), 10 mM ATP, 10 mM L-Proline, 1 mM TCEP; for cryoprotection, crystal-containing drop was diluted approx. four-fold with 30% glycerol, 0.175 M MgCl2, 24.5% PEG 3350, 0.105 M Tris (pH 8.2), 0.7 mM TCEP and crystal was frozen in LN2 after several minutes of equilibration., sitting drop vapor diffusion, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.22 44.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.338 α = 90 b = 87.624 β = 90 c = 142.41 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 100 CCD MarUSA MarMosaic -325 CCD 2008-12-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.97946 SSRL BL9-2
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 40 98.7 0.089 8 4.5 52868 5 36.7
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 2.2 2.28 92.2 0.369 2.8 3.5 4857
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 1NJ5 2.2 30.19 52791 2726 98.72 0.174 0.172 0.1864 0.215 0.2185 RANDOM 34.624
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 -0.1 1.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.365 r_dihedral_angle_4_deg 17.506 r_dihedral_angle_3_deg 12.427 r_dihedral_angle_1_deg 5.89 r_scangle_it 4.163 r_scbond_it 2.741 r_mcangle_it 2.23 r_mcbond_it 1.334 r_angle_refined_deg 1.07 r_angle_other_deg 0.798
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.365 r_dihedral_angle_4_deg 17.506 r_dihedral_angle_3_deg 12.427 r_dihedral_angle_1_deg 5.89 r_scangle_it 4.163 r_scbond_it 2.741 r_mcangle_it 2.23 r_mcbond_it 1.334 r_angle_refined_deg 1.07 r_angle_other_deg 0.798 r_mcbond_other 0.366 r_chiral_restr 0.062 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7924 Nucleic Acid Atoms Solvent Atoms 215 Heterogen Atoms 96
Software Software Software Name Purpose HKL-2000 data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction Blu-Ice data collection HKL-2000 data reduction