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Crystal structure of Trypanosoma cruzi formiminoglutamase N114H variant with Mn2+2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2A0M PDB ENTRY 2A0M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 294 Apo-enzyme was crystallized in the following conditions: a 4 uL drop of protein solution [10 mg/mL protein, 50 mM bicine (pH 8.5), 100 uM MnCl2] was mixed with a 4 uL drop of precipitant solution [25% PEG 3350, 0.1 M sodium acetate (pH 4.6)] on a siliconized cover slide and equilibrated against a 500 uL reservoir of precipitant solution. To obtain the Mn2+ bound form, apo-crystal was soaked in 10 mM MnCl2, 0.1 M sodium malonate (pH 7.5), 27% PEG 3350 for 24 hours, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 1.98 37.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 129.431 α = 90 b = 129.431 β = 90 c = 42.522 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 100 CCD ADSC QUANTUM 315r 2012-10-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1.075 NSLS X29A
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 1.8 50 100 0.088 0.088 18.949 6.3 24658 -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 1.8 1.86 100 0.754 0.754 2.966 6.1
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 2A0M 1.799 30.012 0.18 24658 23858 1211 96.66 0.1897 0.1879 0.1868 0.2215 0.2186 random 36.1
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] -1.9186 -1.9186 3.8372
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 15.352 f_angle_d 1.025 f_chiral_restr 0.076 f_bond_d 0.007 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2285 Nucleic Acid Atoms Solvent Atoms 93 Heterogen Atoms 2
Software Software Software Name Purpose CBASS data collection PHASER phasing PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling