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1-deoxy-D-xylulose 5-phosphate synthase (DXS) from Deinococcus radiodurans
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 298 100 mM Tris, pH7.5, 200 mM ammonium acetate, 150 mM NaCl, and 20% (w/v) PEG 6000 or PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.74 55.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.261 α = 90 b = 154.062 β = 98.91 c = 124.881 γ = 90
Symmetry Space Group P 1 21 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 IMAGE PLATE MAR scanner 180 mm plate 2006-04-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X4C NSLS X4C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) 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 2.9 30 97.4 0.114 0.114 13.4 3.5 65814 64098 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.9 3 96.6 0.42 0.42 3.3 3.4 6571
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.9 30 62969 3206 97.39 0.212 0.209 0.208 0.272 0.2637 RANDOM 25.511
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] -0.67 1.25 4.18 -3.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.588 r_dihedral_angle_3_deg 20.056 r_dihedral_angle_4_deg 18.796 r_dihedral_angle_1_deg 6.589 r_scangle_it 1.721 r_angle_refined_deg 1.382 r_scbond_it 1.012 r_mcangle_it 0.66 r_mcbond_it 0.374 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.588 r_dihedral_angle_3_deg 20.056 r_dihedral_angle_4_deg 18.796 r_dihedral_angle_1_deg 6.589 r_scangle_it 1.721 r_angle_refined_deg 1.382 r_scbond_it 1.012 r_mcangle_it 0.66 r_mcbond_it 0.374 r_nbtor_refined 0.31 r_nbd_refined 0.227 r_symmetry_vdw_refined 0.197 r_xyhbond_nbd_refined 0.162 r_metal_ion_refined 0.142 r_chiral_restr 0.093 r_symmetry_hbond_refined 0.039 r_bond_refined_d 0.011 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16802 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 108
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction MAR345 data collection DENZO data reduction SCALEPACK data scaling MOLREP phasing