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Structure of truncated 1-deoxy-D-xylulose 5-phosphate synthase (DXS) from Deinococcus radiodurans
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2O1X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 0.2 M Calcium acetate hydrate, 0.1 M Tris, 20 % PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.27 45.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.321 α = 90 b = 87.367 β = 90 c = 181.865 γ = 90
Symmetry Space Group P 21 21 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 PILATUS 6M-F 2017-04-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.0332 PETRA III, DESY P11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.099 47.549 99.08 0.913 5.87 2 67987
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.175 99.48 0.444
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 2o1x 2.099 47.549 67497 3427 98.976 0.193 0.1908 0.1908 0.236 0.236 28.734
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] -0.023 0.007 0.016
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.139 r_dihedral_angle_4_deg 15.213 r_dihedral_angle_3_deg 14.664 r_dihedral_angle_1_deg 6.396 r_lrange_it 5.23 r_lrange_other 5.198 r_scangle_it 3.444 r_scangle_other 3.443 r_mcangle_it 2.69 r_mcangle_other 2.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.139 r_dihedral_angle_4_deg 15.213 r_dihedral_angle_3_deg 14.664 r_dihedral_angle_1_deg 6.396 r_lrange_it 5.23 r_lrange_other 5.198 r_scangle_it 3.444 r_scangle_other 3.443 r_mcangle_it 2.69 r_mcangle_other 2.69 r_angle_other_deg 2.343 r_scbond_it 2.093 r_scbond_other 2.089 r_mcbond_it 1.698 r_mcbond_other 1.697 r_angle_refined_deg 1.402 r_metal_ion_refined 0.246 r_symmetry_nbd_refined 0.221 r_symmetry_nbd_other 0.211 r_nbd_other 0.21 r_nbd_refined 0.183 r_symmetry_xyhbond_nbd_refined 0.165 r_xyhbond_nbd_refined 0.157 r_nbtor_refined 0.149 r_symmetry_nbtor_other 0.064 r_chiral_restr 0.062 r_bond_other_d 0.036 r_gen_planes_other 0.007 r_bond_refined_d 0.006 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8274 Nucleic Acid Atoms Solvent Atoms 481 Heterogen Atoms 63
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing Coot model building