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Structural Characterization of Beta Cyanoalanine Synthase from Tetranychus Urticae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6PMU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 277 0.1 M Sodium malonate pH 6, 12% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.15 42.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.801 α = 90 b = 91.801 β = 90 c = 140.122 γ = 90
Symmetry Space Group P 43 21 2
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 2021-02-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0000 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.35 40 99.1 0.098 0.098 0.127 0.037 0.941 17.5 11.5 25330
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.35 2.39 100 0.429 0.42 0.472 0.147 0.941 5 9.8
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6PMU 2.351 39.403 24758 1245 96.598 0.173 0.1708 0.1789 0.2239 0.2314 34.933
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] -1.951 -1.951 3.901
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.529 r_dihedral_angle_4_deg 17.289 r_dihedral_angle_3_deg 13.378 r_lrange_it 6.517 r_lrange_other 6.489 r_dihedral_angle_1_deg 6.468 r_scangle_it 4.873 r_scangle_other 4.872 r_mcangle_it 3.891 r_mcangle_other 3.891
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.529 r_dihedral_angle_4_deg 17.289 r_dihedral_angle_3_deg 13.378 r_lrange_it 6.517 r_lrange_other 6.489 r_dihedral_angle_1_deg 6.468 r_scangle_it 4.873 r_scangle_other 4.872 r_mcangle_it 3.891 r_mcangle_other 3.891 r_scbond_it 3.131 r_scbond_other 3.131 r_mcbond_it 2.595 r_mcbond_other 2.591 r_angle_refined_deg 1.433 r_angle_other_deg 1.306 r_nbd_other 0.253 r_nbd_refined 0.191 r_symmetry_nbd_other 0.182 r_symmetry_nbd_refined 0.18 r_symmetry_xyhbond_nbd_other 0.168 r_nbtor_refined 0.155 r_xyhbond_nbd_refined 0.153 r_ncsr_local_group_1 0.084 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.07 r_symmetry_xyhbond_nbd_refined 0.049 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4541 Nucleic Acid Atoms Solvent Atoms 277 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing