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Structure of the arginase-2-inhibitory human antigen-binding fragment Fab C0020187
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 7.5 291 100 mM HEPES pH 7.5
70% MPD
Crystal Properties Matthews coefficient Solvent content 3.19 61.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.32 α = 90 b = 103.37 β = 90 c = 164.38 γ = 90
Symmetry Space Group C 2 2 21
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 2018-12-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.91587 Diamond I04-1
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 1.78 49.355 99.7 0.16 1 8.1 10.4 58306
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 1.78 1.82 99.1 4.11 0.31 0.5 8.5
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 1.78 49.354 58262 2923 99.598 0.18 0.1781 0.1786 0.2165 0.217 33.211
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] -2.39 3.811 -1.421
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.662 r_dihedral_angle_4_deg 23.295 r_dihedral_angle_1_deg 21.151 r_dihedral_angle_3_deg 14.262 r_lrange_it 7.997 r_lrange_other 7.996 r_scangle_it 6.351 r_scangle_other 6.336 r_scbond_it 4.296 r_scbond_other 4.283
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.662 r_dihedral_angle_4_deg 23.295 r_dihedral_angle_1_deg 21.151 r_dihedral_angle_3_deg 14.262 r_lrange_it 7.997 r_lrange_other 7.996 r_scangle_it 6.351 r_scangle_other 6.336 r_scbond_it 4.296 r_scbond_other 4.283 r_mcangle_it 3.967 r_mcangle_other 3.967 r_mcbond_it 2.902 r_mcbond_other 2.899 r_angle_refined_deg 1.781 r_dihedral_angle_other_3_deg 1.578 r_angle_other_deg 1.451 r_xyhbond_nbd_refined 0.296 r_nbd_other 0.252 r_symmetry_xyhbond_nbd_refined 0.204 r_nbd_refined 0.194 r_symmetry_nbd_other 0.19 r_nbtor_refined 0.167 r_symmetry_nbd_refined 0.158 r_symmetry_nbtor_other 0.087 r_chiral_restr 0.082 r_symmetry_xyhbond_nbd_other 0.031 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3278 Nucleic Acid Atoms Solvent Atoms 318 Heterogen Atoms 64
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing Coot model building