5W99

Pyridine synthase, PbtD, from GE2270 biosynthesis bound to TSP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5W98 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.52821.9 M lithium sulfate, 2% PEG 400, and 0.1 M Tris pH 8.5
Crystal Properties
Matthews coefficientSolvent content
2.2946.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.25α = 90
b = 66.457β = 90
c = 116.572γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300HE2016-07-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.97872APS21-ID-F

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
11.58941.3799.50.132141246922
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)
11.591.695.51.2030.545210.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT5W981.5958.2944486236599.350.163770.161890.19874RANDOM16.5
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]
-0.380.52-0.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.957
r_dihedral_angle_4_deg20.933
r_dihedral_angle_3_deg12.892
r_long_range_B_refined5.978
r_long_range_B_other5.502
r_dihedral_angle_1_deg5.412
r_scangle_other4.188
r_scbond_it2.784
r_scbond_other2.78
r_angle_refined_deg1.818
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.957
r_dihedral_angle_4_deg20.933
r_dihedral_angle_3_deg12.892
r_long_range_B_refined5.978
r_long_range_B_other5.502
r_dihedral_angle_1_deg5.412
r_scangle_other4.188
r_scbond_it2.784
r_scbond_other2.78
r_angle_refined_deg1.818
r_mcangle_other1.699
r_mcangle_it1.698
r_mcbond_it1.212
r_mcbond_other1.199
r_angle_other_deg1.077
r_chiral_restr0.115
r_bond_refined_d0.02
r_gen_planes_refined0.012
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 Atoms2531
Nucleic Acid Atoms
Solvent Atoms442
Heterogen Atoms44

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing