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Structure of the arginase-2-inhibitory human antigen-binding fragment Fab C0021158
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 5 291 100 mM NaAcO pH 5.0
20% PEG6000
200 mM LiCl
Crystal Properties Matthews coefficient Solvent content 2.44 49.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.732 α = 90 b = 122.67 β = 114.891 c = 63.985 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 1.9 48.96 98.3 0.11 1 6.4 3.4 67778
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 1.9 1.94 98.5 1.45 0.53 0.7 3.5
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 1.9 48.955 67745 3129 98.195 0.235 0.2337 0.2336 0.2609 0.2607 40.864
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] 1.237 1.324 -0.705 -1.231
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.935 r_dihedral_angle_4_deg 20.591 r_dihedral_angle_3_deg 15.22 r_dihedral_angle_1_deg 7.643 r_lrange_it 3.974 r_lrange_other 3.973 r_mcangle_other 2.009 r_mcangle_it 2.008 r_scangle_it 1.629 r_scangle_other 1.629
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.935 r_dihedral_angle_4_deg 20.591 r_dihedral_angle_3_deg 15.22 r_dihedral_angle_1_deg 7.643 r_lrange_it 3.974 r_lrange_other 3.973 r_mcangle_other 2.009 r_mcangle_it 2.008 r_scangle_it 1.629 r_scangle_other 1.629 r_angle_refined_deg 1.341 r_angle_other_deg 1.176 r_mcbond_it 1.147 r_mcbond_other 1.143 r_scbond_it 0.943 r_scbond_other 0.943 r_symmetry_xyhbond_nbd_refined 0.26 r_symmetry_xyhbond_nbd_other 0.179 r_nbd_refined 0.176 r_symmetry_nbd_other 0.171 r_nbtor_refined 0.152 r_nbd_other 0.151 r_xyhbond_nbd_refined 0.146 r_symmetry_nbd_refined 0.104 r_ncsr_local_group_2 0.082 r_symmetry_nbtor_other 0.071 r_ncsr_local_group_1 0.07 r_chiral_restr 0.047 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 6449 Nucleic Acid Atoms Solvent Atoms 282 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing Coot model building