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Crystal structure of human beta-ureidopropionase (beta-alanine synthase) - mutant T299C
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VHH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.75 293 16% (w/v) PEG 3350
0.1 M HEPES pH 7.75
300 mM NaSCN
3 mg/ml enzyme variant
Crystal Properties Matthews coefficient Solvent content 2.66 53.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.815 α = 90 b = 104.244 β = 90 c = 102.808 γ = 90
Symmetry Space Group C 2 2 21
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 6M 2017-09-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9762 Diamond I03
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 2.08 28.63 99.6 0.126 0.131 0.036 0.999 14.6 13.4 28448 37.2
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 2.08 2.13 95.1 0.814 0.847 0.232 0.892 3.3 13
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 2VHH 2.08 28.1 26915 1453 99.93 0.17656 0.17539 0.1854 0.1991 0.2075 RANDOM 35.248
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] -1.84 2.32 -0.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.189 r_dihedral_angle_4_deg 16.153 r_dihedral_angle_3_deg 11.34 r_dihedral_angle_1_deg 6.273 r_long_range_B_refined 4.956 r_long_range_B_other 4.853 r_angle_refined_deg 1.322 r_mcangle_it 1.112 r_mcangle_other 1.111 r_angle_other_deg 0.918
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.189 r_dihedral_angle_4_deg 16.153 r_dihedral_angle_3_deg 11.34 r_dihedral_angle_1_deg 6.273 r_long_range_B_refined 4.956 r_long_range_B_other 4.853 r_angle_refined_deg 1.322 r_mcangle_it 1.112 r_mcangle_other 1.111 r_angle_other_deg 0.918 r_scangle_other 0.906 r_mcbond_it 0.619 r_mcbond_other 0.619 r_scbond_it 0.522 r_scbond_other 0.522 r_chiral_restr 0.076 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.002 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 r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2621 Nucleic Acid Atoms Solvent Atoms 208 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing