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Group A Streptococcus GacA is an essential dTDP-4-dehydrorhamnose reductase (RmlD)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD, 0.02 M of each carboxylic acid (0.2 M sodium formate, 0.2 M ammonium acetate, 0.2 M trisodium citrate, 0.2 M sodium potassium L-tartrate, 0.2 M sodium oxamate) and 0.1 M MES/imidazole pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.25 45.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.482 α = 66.3 b = 45.977 β = 81.21 c = 48.867 γ = 95.27
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 2012-11-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.89 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.1 43.8 94.03 22.5 3.7 108172 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.1 1.14 85.5 5.7
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 THROUGHOUT 1.1 43.77 102724 5445 94.03 0.1302 0.1289 0.127 0.15494 0.1528 RANDOM 17.021
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] -0.72 0.29 -0.07 0.59 -0.51 -0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.638 r_dihedral_angle_4_deg 23.087 r_sphericity_free 11.602 r_dihedral_angle_3_deg 11.415 r_rigid_bond_restr 10.222 r_sphericity_bonded 6.647 r_dihedral_angle_1_deg 5.921 r_long_range_B_refined 2.364 r_scangle_other 2.274 r_long_range_B_other 2.227
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.638 r_dihedral_angle_4_deg 23.087 r_sphericity_free 11.602 r_dihedral_angle_3_deg 11.415 r_rigid_bond_restr 10.222 r_sphericity_bonded 6.647 r_dihedral_angle_1_deg 5.921 r_long_range_B_refined 2.364 r_scangle_other 2.274 r_long_range_B_other 2.227 r_angle_refined_deg 2.073 r_scbond_it 1.984 r_scbond_other 1.98 r_mcangle_other 1.74 r_mcangle_it 1.713 r_angle_other_deg 1.529 r_mcbond_it 1.479 r_mcbond_other 1.446 r_chiral_restr 0.275 r_bond_refined_d 0.022 r_gen_planes_refined 0.012 r_gen_planes_other 0.004 r_bond_other_d 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2268 Nucleic Acid Atoms Solvent Atoms 468 Heterogen Atoms 21
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Coot model building PHENIX phasing