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N-Carbamoyl-beta-Alanine Amidohydrolases from Rhizobium radiobacter MDC 8606
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293.15 23 % (w/v) PEG1500 and 100 mM MMT pH 6.0
Crystal Properties Matthews coefficient Solvent content 2.29 46.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.231 α = 90 b = 104.622 β = 90 c = 145.372 γ = 90
Symmetry Space Group P 2 21 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 PILATUS 6M 2019-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.91188 Diamond I04-1
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 84.92 100 0.996 7.1 7 55817
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 2.05 0.786 1.3
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2 84.917 55651 2802 99.801 0.231 0.2287 0.2287 0.2698 0.2698 29.238
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] -0.14 -0.448 0.588
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.663 r_dihedral_angle_3_deg 15.58 r_dihedral_angle_2_deg 12.167 r_dihedral_angle_1_deg 7.757 r_lrange_it 5.012 r_lrange_other 4.993 r_scangle_it 3.483 r_scangle_other 3.483 r_mcangle_it 2.652 r_mcangle_other 2.651
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.663 r_dihedral_angle_3_deg 15.58 r_dihedral_angle_2_deg 12.167 r_dihedral_angle_1_deg 7.757 r_lrange_it 5.012 r_lrange_other 4.993 r_scangle_it 3.483 r_scangle_other 3.483 r_mcangle_it 2.652 r_mcangle_other 2.651 r_scbond_it 2.512 r_scbond_other 2.512 r_mcbond_it 1.855 r_angle_refined_deg 1.851 r_mcbond_other 1.851 r_angle_other_deg 0.706 r_symmetry_nbd_refined 0.221 r_nbd_refined 0.199 r_nbd_other 0.192 r_xyhbond_nbd_refined 0.187 r_nbtor_refined 0.167 r_symmetry_nbd_other 0.166 r_symmetry_xyhbond_nbd_refined 0.1 r_chiral_restr 0.093 r_ncsr_local_group_1 0.087 r_symmetry_nbtor_other 0.079 r_metal_ion_refined 0.04 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 r_bond_other_d 0.003 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6196 Nucleic Acid Atoms Solvent Atoms 362 Heterogen Atoms 28
Software Software Software Name Purpose xia2 data reduction DIALS data reduction Aimless data scaling MoRDa phasing MolProbity model building BUCCANEER model building Coot model building BUSTER refinement REFMAC refinement