2IX4

Arabidopsis thaliana mitochondrial beta-ketoacyl ACP synthase hexanoic acid complex


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1W0IPDB ENTRY 1W0I

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.50.1 M MES-BUFFER PH 6.5, 12% PEG20000, 20 MG/ML HEXANOYL-COA
Crystal Properties
Matthews coefficientSolvent content
2.4650

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.109α = 90
b = 92.942β = 106.59
c = 74.217γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2005-11-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X11EMBL/DESY, HAMBURGX11

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
11.9571.195.60.114.83.76432718.07
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)
11.952.0370.50.381.83.4

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 1W0I1.9571.07643273433990.1970.1950.224RANDOM23.55
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]
-1.12.11-0.622.93
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.714
r_dihedral_angle_4_deg14.583
r_dihedral_angle_3_deg12.714
r_dihedral_angle_1_deg4.876
r_scangle_it1.443
r_angle_refined_deg0.934
r_scbond_it0.832
r_mcangle_it0.494
r_nbtor_refined0.296
r_mcbond_it0.249
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.714
r_dihedral_angle_4_deg14.583
r_dihedral_angle_3_deg12.714
r_dihedral_angle_1_deg4.876
r_scangle_it1.443
r_angle_refined_deg0.934
r_scbond_it0.832
r_mcangle_it0.494
r_nbtor_refined0.296
r_mcbond_it0.249
r_nbd_refined0.183
r_symmetry_vdw_refined0.132
r_symmetry_hbond_refined0.11
r_xyhbond_nbd_refined0.093
r_chiral_restr0.064
r_bond_refined_d0.006
r_gen_planes_refined0.002
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6444
Nucleic Acid Atoms
Solvent Atoms489
Heterogen Atoms16

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing