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Crystal structure of Trypanosoma cruzi formiminoglutamase (oxidized) with Mn2+2 at pH 8.5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4MYF PDB ENTRY 4MYF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 294 An apo-T. cruzi formiminoglutamase (oxidized) crystal was soaked in 20 mM MnCl2, 0.1 M sodium malonate (pH8.5), 27% PEG 3350 for 12 hours, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 1.99 38.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 129.729 α = 90 b = 129.729 β = 90 c = 42.482 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 93 IMAGE PLATE RIGAKU RAXIS IV++ mirrors 2012-09-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.52 50 98.4 0.077 0.077 14.367 3.6 40463 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.52 1.57 95.1 0.422 0.422 2.732 3.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 4MYF 1.518 25.126 0.07 40463 39990 2050 97.2 0.147 0.1462 0.1469 0.1621 0.1558 random
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] -1.5358 -1.5358 3.0716
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 16.703 f_angle_d 1.069 f_chiral_restr 0.072 f_bond_d 0.007 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2209 Nucleic Acid Atoms Solvent Atoms 122 Heterogen Atoms 2
Software Software Software Name Purpose CrystalClear data collection PHASER phasing PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling