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Crystal structure of Leishmania mexicana arginase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4IU0 PDB ENTRY 4IU0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.3 298 3 uL protein solution (7.0 mg/mL delta-12-LmARG, 45 mM bicine, pH 8.5, 1.4 mM thymine, 90 uM manganese chloride, 4.5% v/v glycerol, 1.8 mM BME) + 3 uL precipitant solution (10% w/v PEG10000, 5% v/v MPD, 0.1 M HEPES, pH 7.3) equilibrated against 500 uL precipitant solution on a siliconized cover slide, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.46 50.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.52 α = 90 b = 89.52 β = 90 c = 115.079 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 315 2012-04-18 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 99.8 0.087 0.087 16.91 4.7 31867 31710 -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 0.525 0.525 2.775 4.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 4IU0 1.8 50 31867 30734 2382 96.4 0.144 0.144 0.144 0.142 0.1903 0.1881 RANDOM 36
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] -4.026 -4.026 8.051
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.1 c_scangle_it 2.917 c_mcangle_it 1.929 c_scbond_it 1.91 c_angle_deg 1.4 c_mcbond_it 1.155 c_improper_angle_d 0.8 c_bond_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2361 Nucleic Acid Atoms Solvent Atoms 107 Heterogen Atoms 8
Software Software Software Name Purpose CBASS data collection CNS refinement HKL-2000 data reduction HKL-2000 data scaling CNS phasing