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Structure of Glaciozyma antarctica Arginase Reveals Cold-active Adaptation via Increased Flexible Access to the Active Site
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277 0.1M sodium malonate pH 5, 12 % w/v polyethylene glycol 3,350, 0.1 M TCEP hydrochloride, 10mg/ml purified protein
Crystal Properties Matthews coefficient Solvent content 2.22 44.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.193 α = 90 b = 91.193 β = 90 c = 107.779 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 200K 2016-03-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE Cu FINE FOCUS 1.54178
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.349 63.7 95 0.772 1.6 3.7 13850
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.35 2.53 0.772
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.35 28.784 13781 689 98.994 0.223 0.2206 0.2206 0.2798 0.28 RANDOM 57.643
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] 0.876 0.438 0.876 -2.841
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.308 r_dihedral_angle_6_deg 14.47 r_dihedral_angle_2_deg 10.106 r_dihedral_angle_1_deg 9.494 r_lrange_it 7.412 r_scangle_it 4.307 r_mcangle_it 4.3 r_scbond_it 2.981 r_mcbond_it 2.8 r_angle_refined_deg 2.285
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.308 r_dihedral_angle_6_deg 14.47 r_dihedral_angle_2_deg 10.106 r_dihedral_angle_1_deg 9.494 r_lrange_it 7.412 r_scangle_it 4.307 r_mcangle_it 4.3 r_scbond_it 2.981 r_mcbond_it 2.8 r_angle_refined_deg 2.285 r_nbtor_refined 0.281 r_nbd_refined 0.186 r_chiral_restr 0.176 r_symmetry_nbd_refined 0.16 r_xyhbond_nbd_refined 0.129 r_symmetry_xyhbond_nbd_refined 0.086 r_bond_refined_d 0.01 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2169 Nucleic Acid Atoms Solvent Atoms 46 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing