3DRD

Crystal Structure of 7,8 Diaminopelargonic Acid Synthase Apoenzyme 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
2.1542.66

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.173α = 90
b = 102.844β = 105.15
c = 74.555γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120IMAGE PLATERIGAKU RAXIS IV++2007-02-28MSINGLE 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
12.1739.53930.06326.16.741693
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)
2.172.2963.50.3233.8

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 3BV02.1735395912098930.207960.205020.26498RANDOM27.434
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]
-1.16-0.361.27-0.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.288
r_dihedral_angle_4_deg18.774
r_dihedral_angle_3_deg18.732
r_scangle_it6.633
r_dihedral_angle_1_deg6.371
r_scbond_it4.992
r_mcangle_it3.492
r_mcbond_it2.441
r_angle_refined_deg1.281
r_nbtor_refined0.322
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.288
r_dihedral_angle_4_deg18.774
r_dihedral_angle_3_deg18.732
r_scangle_it6.633
r_dihedral_angle_1_deg6.371
r_scbond_it4.992
r_mcangle_it3.492
r_mcbond_it2.441
r_angle_refined_deg1.281
r_nbtor_refined0.322
r_symmetry_vdw_refined0.241
r_nbd_refined0.234
r_xyhbond_nbd_refined0.2
r_symmetry_hbond_refined0.15
r_chiral_restr0.101
r_bond_refined_d0.009
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6576
Nucleic Acid Atoms
Solvent Atoms250
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
CrystalCleardata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing