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The reaction mechanism of the N-isopropylammelide isopropylaminohydrolase AtzC: insights from structural and mutagenesis studies
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QT3 PDB ENTRY 2QT3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 PROTEIN AT 5.5 MG/ML OVER A RESERVOIR OF 2.5 M MALONATE PH 7.0, 100 MM HEPES BUFFER AT PH 7.5; DROPS WERE 150 NL PLUS 150 NL. IN-SITU THROMBIN TREATMENT WAS USED TO REMOVE THE HIS-TAG.
Crystal Properties Matthews coefficient Solvent content 2.89 57.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.234 α = 90 b = 87.28 β = 103.93 c = 114.364 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC CCD 2013-12-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 Australian Synchrotron MX2
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 2.2 46.3 99.4 0.14 12.5 7.7 51202
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 2.2 2.32 98.9 0.8 2.8 7.7
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 PDB ENTRY 2QT3 2.2 46.37 48598 2603 99.21 0.19695 0.19556 0.1999 0.22311 0.2299 RANDOM 32.228
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] 2.59 0.43 -2.77 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.21 r_dihedral_angle_4_deg 16.852 r_dihedral_angle_3_deg 13.926 r_dihedral_angle_1_deg 5.916 r_mcangle_it 3.321 r_scbond_it 3.127 r_mcbond_it 2.338 r_mcbond_other 2.338 r_angle_refined_deg 1.269 r_angle_other_deg 0.824
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.21 r_dihedral_angle_4_deg 16.852 r_dihedral_angle_3_deg 13.926 r_dihedral_angle_1_deg 5.916 r_mcangle_it 3.321 r_scbond_it 3.127 r_mcbond_it 2.338 r_mcbond_other 2.338 r_angle_refined_deg 1.269 r_angle_other_deg 0.824 r_chiral_restr 0.074 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6275 Nucleic Acid Atoms Solvent Atoms 186 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing