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DAHP synthase complexed with trifluoropyruvate semicarbazone
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5CKS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 277 0.2 M trilithium citrate tetrahydrate
20% (w/v) PEG 3350
1 M MnCl2
2 mM trifluoropyruvate semicarbazone
Crystal Properties Matthews coefficient Solvent content 2.49 50.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 210.281 α = 90 b = 53.2 β = 116.01 c = 150.79 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 PIXEL DECTRIS PILATUS 6M 2016-12-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 0.9794 APS 17-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.5 72.02 99.9 0.111 0.133 0.073 0.991 6.8 3.2 52544 37.23
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.58 99.9 0.418 0.329 0.397 0.801 2.3 3.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5cks 2.5 50.21 1.34 52507 4900 95.53 0.2044 0.2012 0.2017 0.2633 0.2638 43.79
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 21.2411 f_angle_d 1.1158 f_chiral_restr 0.1422 f_plane_restr 0.0144 f_bond_d 0.0097
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10118 Nucleic Acid Atoms Solvent Atoms 122 Heterogen Atoms 56
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing