2NV2

Structure of the PLP synthase complex Pdx1/2 (YaaD/E) from Bacillus subtilis


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2NV1 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP729815-17% PEG 4000, 200mM tri-ammonium citrate pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.754.41

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 93.507α = 90
b = 259.009β = 92.13
c = 144.962γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210ESRF2005-09-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.97626ESRFID29

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
12.125098.20.081123.138891538179829
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)
12.122.1498.40.4432.13.1

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 REPLACEMENTTHROUGHOUT2NV12.12503617941906598.180.148680.146080.19789RANDOM34.093
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]
0.940.31-0.43-0.49
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.262
r_dihedral_angle_4_deg19.123
r_dihedral_angle_3_deg15.956
r_dihedral_angle_1_deg6.246
r_scangle_it3.469
r_scbond_it2.318
r_angle_refined_deg1.452
r_mcangle_it1.383
r_mcbond_it1.043
r_angle_other_deg0.959
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.262
r_dihedral_angle_4_deg19.123
r_dihedral_angle_3_deg15.956
r_dihedral_angle_1_deg6.246
r_scangle_it3.469
r_scbond_it2.318
r_angle_refined_deg1.452
r_mcangle_it1.383
r_mcbond_it1.043
r_angle_other_deg0.959
r_symmetry_hbond_refined0.294
r_symmetry_vdw_other0.287
r_symmetry_vdw_refined0.258
r_nbd_refined0.223
r_nbd_other0.215
r_xyhbond_nbd_refined0.194
r_mcbond_other0.186
r_nbtor_refined0.175
r_xyhbond_nbd_other0.101
r_chiral_restr0.089
r_nbtor_other0.087
r_bond_refined_d0.014
r_gen_planes_refined0.005
r_bond_other_d0.002
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 Atoms41883
Nucleic Acid Atoms
Solvent Atoms5774
Heterogen Atoms203

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing