☰ Navigation Tabs
Crystal structure of human Arginase-1 at pH 9.0 in complex with ABH
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2AEB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4 293 Crystals were generated from 22 % 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 % 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 13 days in soaking solution containing 15 mM ABH.
Crystal Properties Matthews coefficient Solvent content 2.2 44.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.98 α = 90 b = 89.98 β = 90 c = 69.131 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 PILATUS 2M transfocator 2017-09-06 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 1.66 44.99 98.9 0.098 0.126 0.077 0.971 6 2.4 73201 20.47
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 1.66 1.69 97.5 0.736 0.946 0.587 0.385 2.4
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 2AEB 1.66 44.99 69411 3785 98.88 0.14992 0.14833 0.1362 0.17827 0.1656 RANDOM 25.35
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] 4.1 4.1 -8.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.086 r_dihedral_angle_4_deg 16.763 r_dihedral_angle_3_deg 14.081 r_sphericity_bonded 10.765 r_dihedral_angle_1_deg 6.158 r_sphericity_free 5.487 r_long_range_B_refined 4.214 r_long_range_B_other 4.09 r_scangle_other 2.61 r_mcangle_it 2.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.086 r_dihedral_angle_4_deg 16.763 r_dihedral_angle_3_deg 14.081 r_sphericity_bonded 10.765 r_dihedral_angle_1_deg 6.158 r_sphericity_free 5.487 r_long_range_B_refined 4.214 r_long_range_B_other 4.09 r_scangle_other 2.61 r_mcangle_it 2.15 r_mcangle_other 2.15 r_scbond_it 1.727 r_scbond_other 1.725 r_angle_refined_deg 1.524 r_mcbond_it 1.492 r_mcbond_other 1.491 r_angle_other_deg 0.826 r_chiral_restr 0.083 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 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 4720 Nucleic Acid Atoms Solvent Atoms 432 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling MOLREP phasing