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Crystal structure of group A Streptococcal surface dehydrogenase (SDH)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3LVF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 ammonium sulfate, Tris-HCl pH 7.4
Crystal Properties Matthews coefficient Solvent content 2.77 55.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 135.427 α = 90 b = 82.781 β = 102.05 c = 148.921 γ = 90
Symmetry Space Group C 1 2 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 PIXEL DECTRIS PILATUS3 6M 2012-10-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.970 SSRF BL17U1
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 1.739 44.58 99.69 0.048 34.7 3.7 164661
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 1.74 1.8 0.405
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3LVF 1.739 44.58 1.34 164636 8269 99.65 0.1439 0.142 0.151 0.1812 0.1861
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 3.468 f_angle_d 0.814 f_chiral_restr 0.055 f_bond_d 0.006 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10184 Nucleic Acid Atoms Solvent Atoms 1100 Heterogen Atoms 206
Software Software Software Name Purpose PHENIX refinement Blu-Ice data collection HKL-2000 data scaling Coot model building HKL-2000 data reduction MOLREP phasing