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Crystal structure of Leishmania mexicana arginase in complex with inhibitor ABHDP
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, SITTING DROP 294 0.1 M HEPES, pH 7.2, 22% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.4 48.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.934 α = 90 b = 88.934 β = 90 c = 113.867 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 2014-04-23 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) 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 1.65 50 99.5 0.089 22.4 7 40479
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.65 95.3 0.73 0.316 0.817 2.1 5.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE PDB entry 4ITY 1.65 45.783 1.98 40270 2019 99.51 0.189 0.1873 0.1976 0.2125 0.2215
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.693 f_angle_d 0.806 f_chiral_restr 0.028 f_bond_d 0.003 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2312 Nucleic Acid Atoms Solvent Atoms 146 Heterogen Atoms 36
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing CBASS data collection