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Asparaginyl-tRNA synthetase from Brugia malayi complexed with ATP:Mg and L-Asp-beta-NOH adenylate:PPi:Mg
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2XGT PDB ENTRY 2XGT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 ROOM TEMPERATURE HANGING-DROP VAPOUR DIFFUSION IN 0.1 M HEPES PH 8.5, 200MM SODIUM ACETATE USING 17-19 % PEG 4000 AS PRECIPITANT. PROTEIN CONCENTRATION OF 2.5MG/ML WITH 10 MM ATP:MGCL2, 10 MM L-ASP-BETA-NOH.
Crystal Properties Matthews coefficient Solvent content 2.32 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.92 α = 90 b = 106.39 β = 90 c = 161.42 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 ADSC QUANTUM 4r 2003-11-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-3 ESRF ID14-3
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 2.4 50 97.6 0.1 10 3.6 38929
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 2.4 2.49 95.4 0.42 3.3 3.7
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 PDB ENTRY 2XGT 2.4 48.22 37371 1558 100 0.21606 0.21278 0.2108 0.29837 0.2913 RANDOM 29.6
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] 5.48 -1.59 -3.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.885 r_dihedral_angle_4_deg 16.574 r_dihedral_angle_3_deg 16.024 r_dihedral_angle_1_deg 6.341 r_scangle_it 2.064 r_angle_refined_deg 1.356 r_scbond_it 1.318 r_mcangle_it 0.894 r_angle_other_deg 0.863 r_mcbond_it 0.493
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.885 r_dihedral_angle_4_deg 16.574 r_dihedral_angle_3_deg 16.024 r_dihedral_angle_1_deg 6.341 r_scangle_it 2.064 r_angle_refined_deg 1.356 r_scbond_it 1.318 r_mcangle_it 0.894 r_angle_other_deg 0.863 r_mcbond_it 0.493 r_mcbond_other 0.098 r_chiral_restr 0.078 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6968 Nucleic Acid Atoms Solvent Atoms 246 Heterogen Atoms 78
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing