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Crystal structure of AtDHDPS1 in complex with MBDTA-2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6VVI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.1 M HEPES pH 7.5, 0.1 M NaCl, 1.4 M (NH4)2SO4
Crystal Properties Matthews coefficient Solvent content 2.69 54.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.47 α = 90 b = 94.47 β = 90 c = 181.41 γ = 90
Symmetry Space Group P 41 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 2019-11-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.95 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 2.29 20 99.4 0.099 0.1 0.999 27.85 13.1 37390 34.68
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.29 2.43 0.966 0.391 0.407 0.978 7.92 12.8
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 6VVI 2.295 20 37242 1071 99.143 0.184 0.183 0.1824 0.2256 0.2241 44.684
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] 0.887 0.887 -1.774
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.123 r_dihedral_angle_4_deg 17.313 r_dihedral_angle_3_deg 14.943 r_lrange_it 9.879 r_scangle_it 8.89 r_dihedral_angle_1_deg 6.724 r_scbond_it 6.13 r_mcangle_it 4.429 r_mcbond_it 3.424 r_angle_refined_deg 1.415
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.123 r_dihedral_angle_4_deg 17.313 r_dihedral_angle_3_deg 14.943 r_lrange_it 9.879 r_scangle_it 8.89 r_dihedral_angle_1_deg 6.724 r_scbond_it 6.13 r_mcangle_it 4.429 r_mcbond_it 3.424 r_angle_refined_deg 1.415 r_nbtor_refined 0.313 r_symmetry_nbd_refined 0.276 r_nbd_refined 0.207 r_symmetry_xyhbond_nbd_refined 0.2 r_xyhbond_nbd_refined 0.113 r_chiral_restr 0.107 r_bond_refined_d 0.007 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4796 Nucleic Acid Atoms Solvent Atoms 113 Heterogen Atoms 83
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling Auto-Rickshaw phasing