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High resolution crystal structures of Streptococcus pneumoniae nicotinamidase with trapped intermediates provide insights into catalytic mechanism and inhibition by aldehydes
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.3 291 18-22% PEG 3350, 0.2-0.3M NaCl, 0.2M Sodium Malonate, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.24 45.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.838 α = 90 b = 120.875 β = 114.31 c = 63.18 γ = 90
Symmetry Space Group P 1 21 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 315 2008-08-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.9795 APS 24-ID-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.94 50 88.2 0.132 11.3 3.4 54000 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.92 1.95 73.7 0.292 2.2 2.1
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 MOLECULAR REPLACEMENT THROUGHOUT 1.94 41.7 51165 2719 87.03 0.22025 0.21812 0.2171 0.26077 0.2582 RANDOM 24.99
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] 0.11 0.21 -0.04 0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.337 r_dihedral_angle_4_deg 16.72 r_dihedral_angle_3_deg 12.737 r_dihedral_angle_1_deg 4.872 r_scangle_it 1.402 r_angle_refined_deg 0.923 r_scbond_it 0.833 r_mcangle_it 0.664 r_mcbond_it 0.346 r_chiral_restr 0.064
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.337 r_dihedral_angle_4_deg 16.72 r_dihedral_angle_3_deg 12.737 r_dihedral_angle_1_deg 4.872 r_scangle_it 1.402 r_angle_refined_deg 0.923 r_scbond_it 0.833 r_mcangle_it 0.664 r_mcbond_it 0.346 r_chiral_restr 0.064 r_bond_refined_d 0.006 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5792 Nucleic Acid Atoms Solvent Atoms 532 Heterogen Atoms 4
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling