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Tryptophanyl-tRNA synthetase from Cryptosporidium parvum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3FOC PED ENTRY 3FOC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6 293 0.25 M MgCl2, 0.1 M Bis/Tris pH 6.0, 28% PEG 3350, 10mM ATP, 1mM TCEP, 2mM L-tryptophan, vapor diffusion, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.96 37.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.32 α = 90 b = 85.22 β = 101.91 c = 73.11 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 RIGAKU SATURN 944 2008-10-15 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.54
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 2.42 43.07 95.5 0.096 9.7 4.4 25491
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 PED ENTRY 3FOC 2.42 40 24211 1277 94.95 0.22923 0.22693 0.2344 0.27286 0.2807 RANDOM 21.374
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] -3.02 1.38 -1.27 4.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.539 r_dihedral_angle_4_deg 23.271 r_dihedral_angle_3_deg 18.115 r_dihedral_angle_1_deg 6.015 r_scangle_it 1.699 r_angle_refined_deg 1.198 r_scbond_it 1.065 r_angle_other_deg 0.899 r_mcangle_it 0.598 r_mcbond_it 0.317
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.539 r_dihedral_angle_4_deg 23.271 r_dihedral_angle_3_deg 18.115 r_dihedral_angle_1_deg 6.015 r_scangle_it 1.699 r_angle_refined_deg 1.198 r_scbond_it 1.065 r_angle_other_deg 0.899 r_mcangle_it 0.598 r_mcbond_it 0.317 r_mcbond_other 0.074 r_chiral_restr 0.069 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_gen_planes_other 0.002 r_bond_other_d 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5586 Nucleic Acid Atoms Solvent Atoms 44 Heterogen Atoms 30
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction