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Structure of the arginase-2-inhibitory human antigen-binding fragment Fab C0021177
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 MMT (D/L-malic acid, MES, tris)
25% PEG1500
Crystal Properties Matthews coefficient Solvent content 2.17 43.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.537 α = 90 b = 69.244 β = 90 c = 106.517 γ = 90
Symmetry Space Group P 21 21 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 2019-09-25 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 2.25 47.83 100 0.18 1 8.4 12.8 19456
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 2.25 2.32 99.9 4.04 0.36 0.7 13.3
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 2.25 47.505 19407 994 99.943 0.252 0.2482 0.2498 0.3176 0.32 62.164
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] 4.928 -3.131 -1.796
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.373 r_dihedral_angle_3_deg 16.771 r_dihedral_angle_4_deg 9.27 r_dihedral_angle_1_deg 6.759 r_lrange_it 3.153 r_lrange_other 3.153 r_mcangle_it 1.236 r_mcangle_other 1.236 r_angle_refined_deg 1.218 r_angle_other_deg 1.039
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.373 r_dihedral_angle_3_deg 16.771 r_dihedral_angle_4_deg 9.27 r_dihedral_angle_1_deg 6.759 r_lrange_it 3.153 r_lrange_other 3.153 r_mcangle_it 1.236 r_mcangle_other 1.236 r_angle_refined_deg 1.218 r_angle_other_deg 1.039 r_scangle_it 0.734 r_scangle_other 0.734 r_mcbond_it 0.667 r_mcbond_other 0.667 r_scbond_other 0.376 r_scbond_it 0.375 r_nbd_other 0.186 r_nbd_refined 0.172 r_symmetry_xyhbond_nbd_refined 0.163 r_symmetry_nbd_other 0.157 r_nbtor_refined 0.15 r_symmetry_nbd_refined 0.123 r_xyhbond_nbd_refined 0.108 r_symmetry_nbtor_other 0.068 r_chiral_restr 0.031 r_bond_refined_d 0.002 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3201 Nucleic Acid Atoms Solvent Atoms 45 Heterogen Atoms 83
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing