2VB9

beta-ketoacyl-ACP synthase I (KAS) from E. coli, apo structure


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1EK4PDB ENTRY 1EK4

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5CRYSTALLIZATION CONDITIONS: HANGING DROP AGAINST 3% PEG 400, 1.9 M AMMONIUM SULPHATE, 0.1 M TRIS PH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.448

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.914α = 90
b = 138.355β = 90
c = 211.914γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2004-06-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SASLSX06SA

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
11.52099.40.01123.495325313
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)
11.51.6980.513.033.04

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 1EK41.5115.472621111392099.80.1990.1970.238RANDOM20.17
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]
-0.190.66-0.47
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.825
r_dihedral_angle_4_deg17.479
r_dihedral_angle_3_deg13.383
r_dihedral_angle_1_deg5.909
r_scangle_it2.173
r_mcangle_it1.9
r_scbond_it1.555
r_angle_refined_deg1.528
r_mcbond_it1.35
r_nbtor_refined0.304
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.825
r_dihedral_angle_4_deg17.479
r_dihedral_angle_3_deg13.383
r_dihedral_angle_1_deg5.909
r_scangle_it2.173
r_mcangle_it1.9
r_scbond_it1.555
r_angle_refined_deg1.528
r_mcbond_it1.35
r_nbtor_refined0.304
r_symmetry_hbond_refined0.243
r_symmetry_vdw_refined0.223
r_nbd_refined0.214
r_xyhbond_nbd_refined0.209
r_chiral_restr0.099
r_bond_refined_d0.015
r_gen_planes_refined0.007
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 Atoms11870
Nucleic Acid Atoms
Solvent Atoms2334
Heterogen Atoms2

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling