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Crystal structure of putative nucleotide-diphospho-sugar transferase (YP_389115.1) from Desulfovibrio desulfuricans G20 at 1.90 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 NANODROP, 20.0% Glycerol, 0.04M KH2PO4, 16.0% PEG 8000, No Buffer, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.41 48.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.52 α = 90 b = 66.94 β = 90 c = 71.67 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 CCD MARMOSAIC 325 mm CCD Flat collimating mirror, toroid focusing mirror 2008-02-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.97908 SSRL BL9-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.9 28.8 98.8 0.048 10.72 3.57 22017 -3 25.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.97 97.6 0.455 1.95
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 SAD THROUGHOUT 1.9 28.8 21971 1128 99.65 0.173 0.171 0.1763 0.212 0.215 RANDOM 21.842
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] -0.27 0.32 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.582 r_dihedral_angle_4_deg 21.673 r_dihedral_angle_3_deg 12.279 r_scangle_it 7.416 r_scbond_it 5.152 r_dihedral_angle_1_deg 4.756 r_mcangle_it 3.219 r_mcbond_it 1.948 r_angle_refined_deg 1.553 r_angle_other_deg 1.067
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.582 r_dihedral_angle_4_deg 21.673 r_dihedral_angle_3_deg 12.279 r_scangle_it 7.416 r_scbond_it 5.152 r_dihedral_angle_1_deg 4.756 r_mcangle_it 3.219 r_mcbond_it 1.948 r_angle_refined_deg 1.553 r_angle_other_deg 1.067 r_mcbond_other 0.556 r_chiral_restr 0.082 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1809 Nucleic Acid Atoms Solvent Atoms 199 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building XSCALE data scaling PDB_EXTRACT data extraction MAR345 data collection XDS data reduction SHELXD phasing autoSHARP phasing