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The structure of AtzH: a little known member of the atrazine breakdown pathway
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2RCD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 The protein was concentrated to 4 mg/mL and set up with and equal volume of reservoir (150 nL plus 150 nL) with the reservoir contents being: 200 mM ammonium acetate, 30% PEG 4000, 100 mM sodium acetate buffer at pH 5.0
Crystal Properties Matthews coefficient Solvent content 1.84 33.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.465 α = 90 b = 74.977 β = 90 c = 96.221 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 EIGER X 16M 2017-08-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.95374 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.8 51.73 100 0.156 0.063 0.998 11.2 13.3 24359
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.83 100 1.549 0.622 0.837 2.2 13.7
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 2rcd 1.8 51.73 23104 1197 99.86 0.16459 0.16247 0.176 0.20645 0.2203 RANDOM 26.236
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] -1.71 -0.38 2.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.151 r_dihedral_angle_4_deg 18.653 r_dihedral_angle_3_deg 14.948 r_long_range_B_refined 7.985 r_long_range_B_other 7.985 r_dihedral_angle_1_deg 5.543 r_scangle_other 4.553 r_mcangle_it 4.391 r_mcangle_other 4.391 r_scbond_it 2.981
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.151 r_dihedral_angle_4_deg 18.653 r_dihedral_angle_3_deg 14.948 r_long_range_B_refined 7.985 r_long_range_B_other 7.985 r_dihedral_angle_1_deg 5.543 r_scangle_other 4.553 r_mcangle_it 4.391 r_mcangle_other 4.391 r_scbond_it 2.981 r_scbond_other 2.981 r_mcbond_it 2.728 r_mcbond_other 2.698 r_angle_refined_deg 1.677 r_angle_other_deg 1.025 r_chiral_restr 0.103 r_bond_refined_d 0.017 r_gen_planes_refined 0.009 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 2042 Nucleic Acid Atoms Solvent Atoms 178 Heterogen Atoms 19
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing