3DOD

Crystal Structure of PLP Bound 7,8-Diaminopelargonic Acid Synthase in Bacillus subtilis


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3BV0PDB entry 3bv0

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.529120% PEG3350, 0.2M sodium thiocyanate, 5% xylitol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.1342.23

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.674α = 90
b = 104.027β = 105.38
c = 73.868γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120IMAGE PLATERIGAKU RAXIS IV++MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.541

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
11.958.899.10.07210.56.165688
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.91.97980.482.8

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 REPLACEMENTTHROUGHOUTPDB entry 3bv01.93562200333098.470.197940.195710.24022RANDOM48.155
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]
0.890.561.11-1.7
RMS Deviations
KeyRefinement Restraint Deviation
r_angle_refined_deg1.268
r_bond_refined_d0.009
r_dihedral_angle_1_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_chiral_restr
r_gen_planes_refined
r_nbd_refined
r_nbtor_refined
RMS Deviations
KeyRefinement Restraint Deviation
r_angle_refined_deg1.268
r_bond_refined_d0.009
r_dihedral_angle_1_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_chiral_restr
r_gen_planes_refined
r_nbd_refined
r_nbtor_refined
r_xyhbond_nbd_refined
r_symmetry_vdw_refined
r_symmetry_hbond_refined
r_mcbond_it
r_mcangle_it
r_scbond_it
r_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6552
Nucleic Acid Atoms
Solvent Atoms384
Heterogen Atoms30

Software

Software
Software NamePurpose
REFMACrefinement
CrystalCleardata collection
d*TREKdata reduction
d*TREKdata scaling
PHASERphasing