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Structure of arginase-2 in complex with the inhibitory human antigen-binding fragment Fab C0021181
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4HZE 4HZE,6SS0 experimental model PDB 6SS0 4HZE,6SS0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 291 100 mM MMT pH 5.0 (malic acid, MES, tris)
20% glycerol
10% PEG4000
15 mM NaNO3
15 mM Na2HPO4
15 mM (NH4)2SO4
Crystal Properties Matthews coefficient Solvent content 4.25 71.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 150.38 α = 90 b = 150.38 β = 90 c = 110.74 γ = 120
Symmetry Space Group P 3 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M-F 2018-05-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.9184 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 2.9 44.98 100 0.35 1 11 20.2 32384
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.9 3.06 100 5.19 0.32 0.7 20.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4HZE,6SS0 2.9 44.98 32381 1602 99.975 0.268 0.2655 0.1913 0.3181 0.2408 79.623
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] -14.109 -14.109 28.219
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.323 r_dihedral_angle_4_deg 23.645 r_dihedral_angle_3_deg 22.781 r_lrange_it 8.432 r_lrange_other 8.432 r_dihedral_angle_1_deg 8.237 r_mcangle_it 3.846 r_mcangle_other 3.845 r_scangle_it 3.347 r_scangle_other 3.267
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.323 r_dihedral_angle_4_deg 23.645 r_dihedral_angle_3_deg 22.781 r_lrange_it 8.432 r_lrange_other 8.432 r_dihedral_angle_1_deg 8.237 r_mcangle_it 3.846 r_mcangle_other 3.845 r_scangle_it 3.347 r_scangle_other 3.267 r_scbond_it 2.396 r_mcbond_it 2.386 r_mcbond_other 2.384 r_scbond_other 2.341 r_angle_refined_deg 2.012 r_angle_other_deg 1.379 r_symmetry_xyhbond_nbd_refined 0.338 r_symmetry_nbd_refined 0.274 r_nbd_other 0.27 r_symmetry_nbd_other 0.225 r_nbd_refined 0.223 r_xyhbond_nbd_refined 0.218 r_nbtor_refined 0.185 r_symmetry_nbtor_other 0.09 r_symmetry_xyhbond_nbd_other 0.081 r_chiral_restr 0.08 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5619 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing Coot model building