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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 2.23 44.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.171 α = 90 b = 120.752 β = 114.68 c = 62.838 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 2008-03-21 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 1.6 50 97.7 0.051 18.9 4 106300 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) 1.57 1.6 86.2 0.189 3.8 3.4
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 FOURIER SYNTHESIS THROUGHOUT 1.6 41.49 100933 5312 97.73 0.18949 0.18836 0.1865 0.211 0.2092 RANDOM 15.939
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] 0.14 0.98 -0.71 1.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.501 r_dihedral_angle_4_deg 20.993 r_dihedral_angle_3_deg 11.801 r_dihedral_angle_1_deg 4.863 r_scangle_it 1.069 r_angle_refined_deg 0.923 r_scbond_it 0.649 r_mcangle_it 0.513 r_mcbond_it 0.267 r_chiral_restr 0.066
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.501 r_dihedral_angle_4_deg 20.993 r_dihedral_angle_3_deg 11.801 r_dihedral_angle_1_deg 4.863 r_scangle_it 1.069 r_angle_refined_deg 0.923 r_scbond_it 0.649 r_mcangle_it 0.513 r_mcbond_it 0.267 r_chiral_restr 0.066 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5928 Nucleic Acid Atoms Solvent Atoms 838 Heterogen Atoms 40
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling