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Structure of arginase-2 in complex with the inhibitory human antigen-binding fragment Fab C0021158
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6SS4 6SS4, 6SRX experimental model PDB 6SRX 6SS4, 6SRX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 Crystallisation condition:
2 M (NH4)2SO4
Seed condition (approx. final conc.)
20 mM MIB (malonate, imidazole, boric acid)
4% glycerol
2% PEG4000
9 mM NaNO3
9 mM Na2HPO4
9 mM (NH4)2SO4
Crystal Properties Matthews coefficient Solvent content 3.11 60.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 149.061 α = 90 b = 149.061 β = 90 c = 123.287 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 PIXEL DECTRIS PILATUS 6M-F 2019-01-17 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 2.4 45.37 99.9 0.17 0.99 7 5.2 39908
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 2.4 2.49 100 1.72 0.36 1 5.4
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 6SS4, 6SRX 2.4 45.368 39901 1976 99.88 0.255 0.2538 0.1844 0.2842 0.2163 48.54
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] 1.969 1.969 -3.938
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.509 r_dihedral_angle_3_deg 17.55 r_dihedral_angle_4_deg 12.136 r_dihedral_angle_1_deg 7.536 r_lrange_it 4.405 r_lrange_other 4.338 r_mcangle_it 1.704 r_mcangle_other 1.704 r_scangle_it 1.593 r_scangle_other 1.418
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.509 r_dihedral_angle_3_deg 17.55 r_dihedral_angle_4_deg 12.136 r_dihedral_angle_1_deg 7.536 r_lrange_it 4.405 r_lrange_other 4.338 r_mcangle_it 1.704 r_mcangle_other 1.704 r_scangle_it 1.593 r_scangle_other 1.418 r_angle_refined_deg 1.413 r_scbond_it 1.393 r_angle_other_deg 1.137 r_scbond_other 1.122 r_mcbond_it 1.026 r_mcbond_other 1.023 r_nbd_other 0.212 r_symmetry_nbd_refined 0.199 r_nbd_refined 0.189 r_symmetry_xyhbond_nbd_refined 0.18 r_symmetry_nbd_other 0.172 r_xyhbond_nbd_refined 0.166 r_nbtor_refined 0.156 r_symmetry_nbtor_other 0.073 r_chiral_restr 0.054 r_symmetry_xyhbond_nbd_other 0.038 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5680 Nucleic Acid Atoms Solvent Atoms 59 Heterogen Atoms 207
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing Coot model building