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Structure of the arginase-2-inhibitory human antigen-binding fragment Fab C0021181
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6SRV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 291 100 mM SPG pH 7.0
25% PEG1500
PACT A4
SPG: succinic acid, phosphate, glycine
Crystal Properties Matthews coefficient Solvent content 2.13 42.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.4 α = 90 b = 67.37 β = 100.239 c = 94.33 γ = 90
Symmetry Space Group P 1 21 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 2018-11-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.97242 ESRF ID23-1
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 1.7 46.548 100 0.15 1 5.9 6.4 88773
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 1.7 1.73 99.9 2.59 0.36 0.9 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 6SRV 1.7 46.544 88772 4494 99.918 0.191 0.1894 0.1894 0.2242 0.2245 26.241
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] -1.397 -0.389 -0.234 1.662
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.28 r_dihedral_angle_4_deg 20.401 r_dihedral_angle_3_deg 13.464 r_dihedral_angle_1_deg 7.601 r_lrange_it 4.506 r_lrange_other 4.505 r_scangle_it 2.663 r_scangle_other 2.663 r_mcangle_it 2.238 r_mcangle_other 2.237
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.28 r_dihedral_angle_4_deg 20.401 r_dihedral_angle_3_deg 13.464 r_dihedral_angle_1_deg 7.601 r_lrange_it 4.506 r_lrange_other 4.505 r_scangle_it 2.663 r_scangle_other 2.663 r_mcangle_it 2.238 r_mcangle_other 2.237 r_scbond_it 1.657 r_scbond_other 1.657 r_mcbond_it 1.375 r_mcbond_other 1.374 r_angle_refined_deg 1.313 r_angle_other_deg 1.222 r_nbd_other 0.211 r_symmetry_xyhbond_nbd_refined 0.198 r_nbd_refined 0.178 r_symmetry_nbd_other 0.172 r_xyhbond_nbd_refined 0.16 r_nbtor_refined 0.153 r_symmetry_nbd_refined 0.135 r_ncsr_local_group_1 0.096 r_symmetry_nbtor_other 0.072 r_ncsr_local_group_2 0.068 r_chiral_restr 0.052 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 6415 Nucleic Acid Atoms Solvent Atoms 576 Heterogen Atoms 51
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing Coot model building