5AHK

Crystal structure of acetohydroxy acid synthase Pf5 from Pseudomonas protegens


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1YBHPDB ENTRY 1YBH

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.510% (W/V) PEG 4000, 0.1 M MES/IMIDAZOLE PH 6.5, 0.3 M MGCL2, 0.3 M CACL2, 17% (V/V) GLYCEROL
Crystal Properties
Matthews coefficientSolvent content
2.2846

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.22α = 90
b = 139.87β = 97.87
c = 65.34γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2013-03-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.1BESSY14.1

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
11.5549.290.90.07103.41518152
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)
11.551.5881.60.582.33.4

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 1YBH1.5549.22144040773290.210.152270.15110.1739RANDOM17.199
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]
-3.072.877.44-4.38
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.366
r_dihedral_angle_4_deg14.941
r_dihedral_angle_3_deg13.353
r_dihedral_angle_1_deg6.383
r_long_range_B_refined3.116
r_long_range_B_other2.974
r_angle_refined_deg1.422
r_scangle_other1.094
r_angle_other_deg1.011
r_mcangle_it0.929
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.366
r_dihedral_angle_4_deg14.941
r_dihedral_angle_3_deg13.353
r_dihedral_angle_1_deg6.383
r_long_range_B_refined3.116
r_long_range_B_other2.974
r_angle_refined_deg1.422
r_scangle_other1.094
r_angle_other_deg1.011
r_mcangle_it0.929
r_mcangle_other0.928
r_scbond_it0.692
r_scbond_other0.692
r_mcbond_it0.551
r_mcbond_other0.551
r_chiral_restr0.084
r_bond_refined_d0.01
r_gen_planes_refined0.008
r_bond_other_d0.004
r_gen_planes_other0.003
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8530
Nucleic Acid Atoms
Solvent Atoms871
Heterogen Atoms160

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing