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Crystal Structure of NadC from Streptococcus pyogenes
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5HUO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.5 293 0.48 M Ammonium Sulfate, 25% PEG 6000,
0.1 M BIS-TRIS
Crystal Properties Matthews coefficient Solvent content 2.74 55.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.149 α = 90 b = 188.816 β = 90 c = 222.181 γ = 90
Symmetry Space Group C 2 2 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 ADSC QUANTUM 210r 2015-10-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.97919 APS 19-BM
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 3.4 20 81.6 0.107 0.107 15.4 3.5 25907 -3
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 3.4 3.46 95.2 0.606 3.3 3.6
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 5HUO 3.42 20 23334 1221 78.86 0.23569 0.23279 0.2328 0.29354 0.2905 RANDOM 86.544
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] 5.39 -1.95 -3.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.741 r_dihedral_angle_4_deg 17.953 r_dihedral_angle_3_deg 15.831 r_long_range_B_refined 10.773 r_long_range_B_other 10.773 r_dihedral_angle_1_deg 5.978 r_scangle_other 5.479 r_mcangle_it 4.796 r_mcangle_other 4.796 r_scbond_it 3.261
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.741 r_dihedral_angle_4_deg 17.953 r_dihedral_angle_3_deg 15.831 r_long_range_B_refined 10.773 r_long_range_B_other 10.773 r_dihedral_angle_1_deg 5.978 r_scangle_other 5.479 r_mcangle_it 4.796 r_mcangle_other 4.796 r_scbond_it 3.261 r_scbond_other 3.201 r_mcbond_it 2.844 r_mcbond_other 2.844 r_angle_other_deg 1.814 r_angle_refined_deg 1.558 r_chiral_restr 0.08 r_bond_refined_d 0.013 r_bond_other_d 0.01 r_gen_planes_refined 0.009 r_gen_planes_other 0.008 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12666 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 85
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling HKL-2000 data reduction REFMAC phasing