1S06

Crystal Structure of the R253K Mutant of 7,8-Diaminopelargonic Acid Synthase


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5PEG4000, MPD, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 100K
Crystal Properties
Matthews coefficientSolvent content
2.0840.76

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.08α = 90
b = 56.527β = 96.32
c = 120.993γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2002-09-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX II BEAMLINE I7111.13MAX III711

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
12.22099.20.124113.5399453962626.9
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)
2.22.3298.20.4212.43.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTWT dimer2.2203721237212201098.210.1930.193270.1910.22567RANDOM25.122
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]
-0.310.63.3-2.85
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg18.25
r_dihedral_angle_1_deg3.824
r_scangle_it2.955
r_scbond_it1.739
r_angle_refined_deg1.592
r_angle_other_deg1.183
r_mcangle_it1.075
r_mcbond_it0.573
r_symmetry_hbond_other0.503
r_symmetry_hbond_refined0.497
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg18.25
r_dihedral_angle_1_deg3.824
r_scangle_it2.955
r_scbond_it1.739
r_angle_refined_deg1.592
r_angle_other_deg1.183
r_mcangle_it1.075
r_mcbond_it0.573
r_symmetry_hbond_other0.503
r_symmetry_hbond_refined0.497
r_symmetry_vdw_other0.468
r_symmetry_vdw_refined0.416
r_nbtor_other0.298
r_nbd_refined0.268
r_nbd_other0.212
r_xyhbond_nbd_refined0.156
r_xyhbond_nbd_other0.1
r_chiral_restr0.084
r_bond_refined_d0.014
r_gen_planes_refined0.005
r_gen_planes_other0.003
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6666
Nucleic Acid Atoms
Solvent Atoms336
Heterogen Atoms2

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
SFALLphasing