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Crystal structure of Leishmania mexicana arginase in complex with catalytic product L-ornithine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4ITY PDB ENTRY 4ITY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 298 3 uL protein solution (7.0 mg/mL delta-12-LmARG, 45 mM bicine, pH 8.5, 10 mM DL-alpha-difluoromethylornithine (DFMO), 90 uM manganese chloride, 4.5% v/v glycerol, 1.8 mM BME) + 3 uL precipitant solution (0.1 M HEPES, pH 7.5, 12% w/v PEG3350) equilibrated against 500 uL precipitant solution on a siliconized cover slide, crystals grow within one week, soaked in 10 uL 50 mM L-ornithine, 0.1 M HEPPS, pH 8.5, 15% w/v PEG3350 for 23 hours, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.45 49.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.617 α = 90 b = 89.617 β = 90 c = 114.359 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 1.95 50 99.9 0.077 0.077 20.195 4.7 24954 24877 -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 1.95 2.02 100 0.624 0.624 2.711 4.6
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 4ITY 1.95 50 24954 23754 2181 95.2 0.1643 0.1643 0.1643 0.1633 0.2064 0.2017 RANDOM 53
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] -5.278 -5.278 10.557
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.3 c_scangle_it 3.038 c_mcangle_it 2.894 c_scbond_it 1.894 c_mcbond_it 1.616 c_angle_deg 1.4 c_improper_angle_d 0.87 c_bond_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2361 Nucleic Acid Atoms Solvent Atoms 68 Heterogen Atoms 17
Software Software Software Name Purpose CBASS data collection CNS refinement HKL-2000 data reduction HKL-2000 data scaling CNS phasing