5W98

Pyridine synthase, PbtD, from GE2270 biosynthesis


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.528215% MPD, 8% PEG 6K, 0.1 M MES pH 6.5
Crystal Properties
Matthews coefficientSolvent content
2.1843.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.247α = 90
b = 88.132β = 109.78
c = 44.473γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2015-04-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.97857APS21-ID-G

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.22744.196.50.09110.96.190136
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.231.2583.90.8270.3682.25.7

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 DIFFRACTIONSADTHROUGHOUT1.2344.0785777432096.410.163630.162490.18617RANDOM17.92
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]
0.210.22-0.820.36
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.806
r_dihedral_angle_4_deg21.399
r_dihedral_angle_3_deg12.474
r_long_range_B_refined6.061
r_dihedral_angle_1_deg5.626
r_long_range_B_other5.548
r_scangle_other4.213
r_scbond_it2.858
r_scbond_other2.857
r_mcangle_it2.416
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.806
r_dihedral_angle_4_deg21.399
r_dihedral_angle_3_deg12.474
r_long_range_B_refined6.061
r_dihedral_angle_1_deg5.626
r_long_range_B_other5.548
r_scangle_other4.213
r_scbond_it2.858
r_scbond_other2.857
r_mcangle_it2.416
r_mcangle_other2.416
r_angle_refined_deg2.264
r_mcbond_it1.643
r_mcbond_other1.643
r_angle_other_deg1.141
r_chiral_restr0.26
r_bond_refined_d0.027
r_gen_planes_refined0.013
r_bond_other_d0.002
r_gen_planes_other0.002
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2372
Nucleic Acid Atoms
Solvent Atoms370
Heterogen Atoms12

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
AutoSolphasing