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Entamoeba histolytica asparaginyl-tRNA synthetase (AsnRS) in complex with asparaginyl-adenylate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1X56 1x56, protein only model prepared using CHAINSAW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 298 1 ul 22 mg/ml protein in SGPP buffer mixed with 1 ul well soln. (100 mM Bis-Tris pH 5.5, 28% PEG 3350, 240 mM ammonium sulfate), drop supplemented with 10 mM L-asparagine + 10 mM ATP + 10 mM MgCl2 + 5 mM DTT; cryoprotected by quick dip in well soln containing 30% PEG 3350 and supplemented with 15% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.52 51.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.426 α = 90 b = 58.816 β = 90.45 c = 181.259 γ = 90
Symmetry Space Group P 1 21 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 MARMOSAIC 325 mm CCD 2009-08-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.979 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 2.83 50 100 0.062 14.9 4.6 50783 3 73
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) 2.83 2.93 100 0.459 2.7 4.6 5048
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 1x56, protein only model prepared using CHAINSAW 2.83 41.36 50772 2577 99.79 0.202 0.199 0.1986 0.247 0.2438 RANDOM 75.533
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] 4.52 -1.73 0.19 -4.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.165 r_dihedral_angle_4_deg 17.763 r_dihedral_angle_3_deg 14.71 r_dihedral_angle_1_deg 5.651 r_scangle_it 2.884 r_scbond_it 1.796 r_mcangle_it 1.641 r_angle_refined_deg 0.985 r_mcbond_it 0.902 r_angle_other_deg 0.772
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.165 r_dihedral_angle_4_deg 17.763 r_dihedral_angle_3_deg 14.71 r_dihedral_angle_1_deg 5.651 r_scangle_it 2.884 r_scbond_it 1.796 r_mcangle_it 1.641 r_angle_refined_deg 0.985 r_mcbond_it 0.902 r_angle_other_deg 0.772 r_mcbond_other 0.24 r_chiral_restr 0.058 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 13902 Nucleic Acid Atoms Solvent Atoms 2 Heterogen Atoms 196
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction Blu-Ice data collection HKL-2000 data reduction HKL-2000 data scaling