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Urethanase umg-sp1 without inhibitor or substrate displays flexible active site loops
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, SITTING DROP 8.5 293 30% (v/v) isopropanol, 0.2 M ammonium acetate, 0.1 M Tris pH 8.5
Cryo: 10% glycerol added
Crystal Properties Matthews coefficient Solvent content 2.06 40
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.175 α = 89.994 b = 76.792 β = 112.646 c = 95.068 γ = 113.64
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 EIGER X 16M 2023-09-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.9763 PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.67 45 97.5 0.35 0.99 6.1 8.9 44551 -3 65
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.67 2.85 97.5 2.18 0.53 1.3 9.3
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 FREE R-VALUE 2.67 44.538 44199 2194 97.062 0.263 0.2603 0.2623 0.3227 0.3214 random selection 56.551
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] 3.331 1.459 1.298 -0.957 0.271 -3.201
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.853 r_dihedral_angle_6_deg 14.558 r_lrange_it 11.977 r_lrange_other 11.977 r_dihedral_angle_2_deg 10.834 r_mcangle_other 8.638 r_mcangle_it 8.637 r_scangle_it 8.468 r_scangle_other 8.467 r_dihedral_angle_1_deg 7.753
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.853 r_dihedral_angle_6_deg 14.558 r_lrange_it 11.977 r_lrange_other 11.977 r_dihedral_angle_2_deg 10.834 r_mcangle_other 8.638 r_mcangle_it 8.637 r_scangle_it 8.468 r_scangle_other 8.467 r_dihedral_angle_1_deg 7.753 r_mcbond_it 5.649 r_mcbond_other 5.645 r_scbond_it 5.396 r_scbond_other 5.393 r_angle_refined_deg 1.865 r_angle_other_deg 0.632 r_symmetry_nbd_refined 0.353 r_symmetry_xyhbond_nbd_refined 0.256 r_nbd_other 0.252 r_nbd_refined 0.234 r_symmetry_nbd_other 0.198 r_nbtor_refined 0.177 r_xyhbond_nbd_refined 0.141 r_symmetry_nbtor_other 0.086 r_chiral_restr 0.085 r_ncsr_local_group_2 0.075 r_ncsr_local_group_1 0.072 r_ncsr_local_group_5 0.065 r_ncsr_local_group_6 0.065 r_ncsr_local_group_3 0.062 r_ncsr_local_group_4 0.05 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10821 Nucleic Acid Atoms Solvent Atoms 3 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing