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Crystal structure of C171A Mutant of N-carbamyl-D-amino acid amidohydrolase complexed with N-carbamyl-D-Hydroxyphenylglycine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 PEG3350, BIS-TRIS, Ammonium acetate, calcium chloride
Crystal Properties Matthews coefficient Solvent content 2.07 40.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.165 α = 91.4 b = 79.865 β = 98.48 c = 91.07 γ = 92.78
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 Bruker PHOTON II 2022-03-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE BRUKER D8 QUEST 1.54184
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.52 46.59 98 0.14 7.3 3 72971
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.52 2.57 0.433
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 (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 2.52 46.59 69433 3537 98.04 0.21987 0.2181 0.2023 0.25324 0.232 RANDOM 22.847
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] -11.65 -3.22 -11.71 -3.9 -0.58 15.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.839 r_dihedral_angle_4_deg 18.596 r_dihedral_angle_3_deg 14.813 r_dihedral_angle_1_deg 7.568 r_long_range_B_refined 4.871 r_long_range_B_other 4.856 r_scangle_other 3.111 r_mcangle_it 3.074 r_mcangle_other 3.074 r_scbond_it 2.008
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.839 r_dihedral_angle_4_deg 18.596 r_dihedral_angle_3_deg 14.813 r_dihedral_angle_1_deg 7.568 r_long_range_B_refined 4.871 r_long_range_B_other 4.856 r_scangle_other 3.111 r_mcangle_it 3.074 r_mcangle_other 3.074 r_scbond_it 2.008 r_scbond_other 2.007 r_mcbond_it 1.979 r_mcbond_other 1.978 r_angle_refined_deg 1.436 r_angle_other_deg 1.155 r_chiral_restr 0.062 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 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 r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 19127 Nucleic Acid Atoms Solvent Atoms 270 Heterogen Atoms 120
Software Software Software Name Purpose Aimless data scaling REFMAC refinement