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Structure of arginase-2 in complex with the inhibitory human antigen-binding fragment Fab C0020187
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4HZE 4HZE,6SS5 experimental model PDB 6SS5 4HZE,6SS5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 2 M (NH4)2SO4
Crystal Properties Matthews coefficient Solvent content 2.96 58.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 138.126 α = 90 b = 138.126 β = 90 c = 551.307 γ = 120
Symmetry Space Group P 65 2 2
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 2017-09-18 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 3.25 48.78 100 0.78 0.99 4.2 10.4 50453
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 3.25 3.36 100 8.48 0.5 0.4 9.9
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 4HZE,6SS5 3.25 48.755 50320 2549 99.901 0.303 0.3003 0.3003 0.3606 0.3611 99.097
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] -4.897 -2.448 -4.897 15.886
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.811 r_dihedral_angle_3_deg 22.106 r_dihedral_angle_4_deg 18.707 r_lrange_it 15.185 r_lrange_other 15.185 r_mcangle_it 7.82 r_mcangle_other 7.82 r_dihedral_angle_1_deg 6.723 r_scangle_other 6.519 r_scangle_it 6.507
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.811 r_dihedral_angle_3_deg 22.106 r_dihedral_angle_4_deg 18.707 r_lrange_it 15.185 r_lrange_other 15.185 r_mcangle_it 7.82 r_mcangle_other 7.82 r_dihedral_angle_1_deg 6.723 r_scangle_other 6.519 r_scangle_it 6.507 r_mcbond_it 4.602 r_mcbond_other 4.601 r_scbond_it 3.675 r_scbond_other 3.673 r_angle_refined_deg 1.463 r_angle_other_deg 1.17 r_symmetry_xyhbond_nbd_refined 0.318 r_nbd_other 0.315 r_symmetry_nbd_refined 0.312 r_ncsr_local_group_9 0.226 r_ncsr_local_group_8 0.225 r_nbd_refined 0.223 r_symmetry_nbd_other 0.219 r_xyhbond_nbd_refined 0.204 r_ncsr_local_group_5 0.193 r_ncsr_local_group_6 0.189 r_ncsr_local_group_2 0.186 r_ncsr_local_group_3 0.181 r_ncsr_local_group_4 0.173 r_ncsr_local_group_1 0.166 r_nbtor_refined 0.163 r_ncsr_local_group_7 0.146 r_symmetry_xyhbond_nbd_other 0.137 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.06 r_gen_planes_refined 0.006 r_bond_refined_d 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16814 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 141
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing Coot model building