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Crystal structure of human Arginase-1 at pH 9.0 in complex with CB-1158/INCB001158
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6Q9P
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4 293 Crystals were generated from 22.5 % PEG 1500, 0.2 M MIB buffer pH 4.0 (sodium malonate, imidazole and boric acid in a 2:3:3 molar ratio). Crystals were equilibrated to soaking solution (22.5 % PEG 1500, 0.2 M MMT buffer pH 9.0 (DL-malic acid, MES, Tris base in a 1:2:2 molar ratio). Subsequently, crystals were gradually soaked for 4 days in soaking solution containing 15 mM compound 3.
Crystal Properties Matthews coefficient Solvent content 2.2 44.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.13 α = 90 b = 90.13 β = 90 c = 69.111 γ = 120
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 PILATUS3 2M transfocator 2017-12-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.966 ESRF MASSIF-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.61 51.74 96.9 0.058 0.076 0.049 0.996 6.9 2 79090 20.01
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.61 1.64 96 0.658 0.868 0.561 0.368 2.1
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6Q9P 1.61 51.74 74978 4105 96.85 0.149 0.14744 0.1265 0.177 0.1496 RANDOM 24.684
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] 3.48 3.48 -6.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.348 r_dihedral_angle_4_deg 14.635 r_dihedral_angle_3_deg 12.91 r_dihedral_angle_1_deg 6.164 r_sphericity_bonded 5.325 r_sphericity_free 4.94 r_long_range_B_refined 3.683 r_long_range_B_other 3.657 r_scangle_other 1.999 r_mcangle_it 1.991
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.348 r_dihedral_angle_4_deg 14.635 r_dihedral_angle_3_deg 12.91 r_dihedral_angle_1_deg 6.164 r_sphericity_bonded 5.325 r_sphericity_free 4.94 r_long_range_B_refined 3.683 r_long_range_B_other 3.657 r_scangle_other 1.999 r_mcangle_it 1.991 r_mcangle_other 1.991 r_angle_refined_deg 1.356 r_mcbond_it 1.277 r_mcbond_other 1.277 r_scbond_it 1.274 r_scbond_other 1.266 r_angle_other_deg 0.806 r_chiral_restr 0.077 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4830 Nucleic Acid Atoms Solvent Atoms 376 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling MOLREP phasing