3O93

High resolution crystal structures of Streptococcus pneumoniae nicotinamidase with trapped intermediates provide insights into catalytic mechanism and inhibition by aldehydes


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.329118-22% PEG 3350, 0.2-0.3M NaCl, 0.2M Sodium Malonate, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.2745.73

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.178α = 90
b = 121.167β = 114.55
c = 63.201γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152008-03-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-C0.9795APS24-ID-C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.845099.50.09916.55.4693002
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.841.8798.80.2894.54.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT1.8433.0566829354297.810.210580.209210.23631RANDOM19.968
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]
0.030.08-0.010.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.343
r_dihedral_angle_4_deg20.125
r_dihedral_angle_3_deg12.214
r_dihedral_angle_1_deg4.976
r_scangle_it1.382
r_angle_refined_deg0.947
r_scbond_it0.837
r_mcangle_it0.627
r_mcbond_it0.33
r_chiral_restr0.067
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.343
r_dihedral_angle_4_deg20.125
r_dihedral_angle_3_deg12.214
r_dihedral_angle_1_deg4.976
r_scangle_it1.382
r_angle_refined_deg0.947
r_scbond_it0.837
r_mcangle_it0.627
r_mcbond_it0.33
r_chiral_restr0.067
r_bond_refined_d0.006
r_gen_planes_refined0.003
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 AtomsNumber
Protein Atoms5962
Nucleic Acid Atoms
Solvent Atoms566
Heterogen Atoms4

Software

Software
Software NamePurpose
ADSCdata collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling