2QNX

Crystal structure of the complex between the mycobacterium beta-ketoacyl-acyl carrier protein synthase III (FABH) and 11-[(decyloxycarbonyl)dithio]-undecanoic acid


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1HZPPDB ENTRY 1HZP

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5293100 MM NA MES, 50 MM NAH2PO4/ KH2PO4,1.8M NACL , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.5250.73

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.285α = 90
b = 88.981β = 90
c = 230.252γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IVRIGAKU VARIMAX CONFOCAL OPTICS2006-03-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-0071.5418

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
12.729.0697.30.128.73.65197471921935.4
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)
12.72.8980.2644.83.691952

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1HZP2.7151958719126195497.650.213430.20890.25377RANDOM26.782
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]
3.14-3.320.19
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.356
r_dihedral_angle_4_deg19.169
r_dihedral_angle_3_deg17.383
r_dihedral_angle_1_deg5.228
r_angle_refined_deg1.112
r_scangle_it1.005
r_scbond_it0.607
r_mcangle_it0.426
r_nbtor_refined0.303
r_mcbond_it0.238
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.356
r_dihedral_angle_4_deg19.169
r_dihedral_angle_3_deg17.383
r_dihedral_angle_1_deg5.228
r_angle_refined_deg1.112
r_scangle_it1.005
r_scbond_it0.607
r_mcangle_it0.426
r_nbtor_refined0.303
r_mcbond_it0.238
r_nbd_refined0.207
r_symmetry_hbond_refined0.19
r_xyhbond_nbd_refined0.144
r_symmetry_vdw_refined0.137
r_chiral_restr0.069
r_bond_refined_d0.007
r_gen_planes_refined0.003
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 Atoms4785
Nucleic Acid Atoms
Solvent Atoms110
Heterogen Atoms56

Software

Software
Software NamePurpose
REFMACrefinement
CNSrefinement
AMoREphasing
CrystalCleardata collection
d*TREKdata reduction
d*TREKdata scaling
CNSphasing