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Crystal Structure of Prolyl-tRNA Synthetase from Cryptosporidium parvum complexed with L-Proline and AMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4HVC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 290 CrpaA.18681.a.B3.PW37711 at 21.5 mg/mlprotein was incubated with 3 mM MgCl2, L-proline, and AMPPNP, then mixed 1:1 with Morpheus(c5): 10% (w/v) PEG-20,000, 20% (w/v) PEG MME 550, 0.1 M MOPS/ HEPES-Na, pH = 7.5, 0.03 M each sodium nitrate, disodium hydrogen phosphate, ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.69 54.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.87 α = 90 b = 110.14 β = 90 c = 127.71 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 MARMOSAIC 225 mm CCD Beryllium Lenses 2015-07-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.8 50 99.9 0.083 0.091 19.67 6.2 32278 -3 47.65
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.87 100 0.582 0.635 3.52
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4HVC 2.8 46.611 30839 1881 95.65 0.2156 0.2137 0.2155 0.2434 0.2409 50.6131
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 f_dihedral_angle_d 12.149 f_angle_d 0.511 f_chiral_restr 0.044 f_plane_restr 0.004 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7332 Nucleic Acid Atoms Solvent Atoms 35 Heterogen Atoms 69
Software Software Software Name Purpose XSCALE data scaling PHENIX refinement PDB_EXTRACT data extraction XDS data reduction MoRDa phasing