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Crystal structure of Streptococcus pneumoniae D39 neuraminidase A precursor (NanA)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 294 100 mM Hepes, 30% Jeffamine ED-2001, the drops also contained trypsin at 5000:1 protein/trypsin ratio, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.14 42.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 158.04 α = 90 b = 47.67 β = 116.56 c = 137.27 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 CCD ADSC QUANTUM 4 MIRRORS 2008-04-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X4A 0.9798 NSLS X4A
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 1.7 30 92.7 0.041 34.8688 3.4 98994 11.3
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) 1.7 1.76 89.6 0.094 14.8 3.2 17814
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 (All) 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 1.7 27.39 98994 13133 92.4 0.172 0.172 0.172 0.1768 0.198 0.2018 RANDOM 15.5
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] -2.02 0.73 0.94 1.08
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 25.9 c_scangle_it 2.51 c_scbond_it 1.87 c_mcangle_it 1.62 c_angle_deg 1.4 c_mcbond_it 1.2 c_improper_angle_d 0.81 c_bond_d 0.005 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 25.9 c_scangle_it 2.51 c_scbond_it 1.87 c_mcangle_it 1.62 c_angle_deg 1.4 c_mcbond_it 1.2 c_improper_angle_d 0.81 c_bond_d 0.005 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7518 Nucleic Acid Atoms Solvent Atoms 1745 Heterogen Atoms
Software Software Software Name Purpose ADSC data collection SnB phasing CNS refinement DENZO data reduction SCALEPACK data scaling