2NV1

Structure of the synthase subunit Pdx1 (YaaD) of PLP synthase from Bacillus subtilis


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1ZNN 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.829815-20% ethanol, 200mM MgCl2, 100mM Tris, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.4750.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 101.055α = 90
b = 106.202β = 90
c = 182.332γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4ESRF2005-04-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.97625ESRFID23-1

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
12.085098.60.10393.311830311659425
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)
12.082.199.50.4792.13.3

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 REPLACEMENTTHROUGHOUT1ZNN2.0848.68110798578298.590.144140.141630.19139RANDOM28.452
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]
0.25-0.07-0.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.496
r_dihedral_angle_3_deg12.798
r_dihedral_angle_4_deg9.751
r_dihedral_angle_1_deg6.043
r_scangle_it3.972
r_scbond_it2.616
r_mcangle_it1.603
r_angle_refined_deg1.506
r_mcbond_it1.03
r_angle_other_deg0.976
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.496
r_dihedral_angle_3_deg12.798
r_dihedral_angle_4_deg9.751
r_dihedral_angle_1_deg6.043
r_scangle_it3.972
r_scbond_it2.616
r_mcangle_it1.603
r_angle_refined_deg1.506
r_mcbond_it1.03
r_angle_other_deg0.976
r_symmetry_vdw_other0.296
r_nbd_refined0.232
r_symmetry_hbond_refined0.232
r_mcbond_other0.214
r_nbd_other0.212
r_xyhbond_nbd_refined0.21
r_symmetry_vdw_refined0.182
r_nbtor_refined0.173
r_chiral_restr0.09
r_nbtor_other0.088
r_xyhbond_nbd_other0.086
r_bond_refined_d0.017
r_gen_planes_refined0.006
r_bond_other_d0.003
r_gen_planes_other0.001
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11340
Nucleic Acid Atoms
Solvent Atoms2367
Heterogen Atoms68

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing