☰ Navigation Tabs
Entamoeba histolytica asparaginyl-tRNA synthetase (AsnRS)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3M4P 3m4p; A chain, protein only model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.6 298 0.2 ul 29 mg/ml protein in SGPP buffer mixed with 0.2 ul well soln. (100 mM HEPES pH 7.6, 25% PEG 3350, 200 mM MgCl2); cryoprotected by soaking ~1 min. in well soln supplemented with 10% PEG 200, vapor diffusion, sitting drop, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.54 51.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.047 α = 90 b = 102.047 β = 90 c = 205.015 γ = 90
Symmetry Space Group P 41 21 2
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 2008-04-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.979 SSRL BL11-1
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 3 50 99.8 0.121 9.2 13.9 22471 5 76
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) 3 3.11 98.9 0.762 1.75 10.8 2174
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 3m4p; A chain, protein only model 3 45.8 22380 1144 99.66 0.222 0.22 0.2158 0.267 0.262 RANDOM 87.156
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] 3.41 3.41 -6.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.966 r_dihedral_angle_4_deg 17.304 r_dihedral_angle_3_deg 13.93 r_dihedral_angle_1_deg 5.494 r_scangle_it 2.376 r_scbond_it 1.475 r_mcangle_it 1.349 r_angle_refined_deg 0.958 r_angle_other_deg 0.765 r_mcbond_it 0.754
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.966 r_dihedral_angle_4_deg 17.304 r_dihedral_angle_3_deg 13.93 r_dihedral_angle_1_deg 5.494 r_scangle_it 2.376 r_scbond_it 1.475 r_mcangle_it 1.349 r_angle_refined_deg 0.958 r_angle_other_deg 0.765 r_mcbond_it 0.754 r_mcbond_other 0.2 r_chiral_restr 0.056 r_bond_refined_d 0.006 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 6742 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
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