4NHD

Crystal structure of beta-ketoacyl-ACP synthase III (FabH) from Vibrio Cholerae in complex with Coenzyme A


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2GYOPDB ENTRY 2GYO

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION2890.2M calcium chloride, 20%PEG3350, VAPOR DIFFUSION, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.4349.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 99.449α = 90
b = 100.248β = 90
c = 132.763γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 300 mm plateMIRRORS2013-10-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.9792APS21-ID-G

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
11.785097.60.09125.26.8125028-319.6
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)
11.781.8187.80.81725.45576

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 2GYO1.78501248936293980.17150.17020.1957RANDOM26.2697
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]
-0.67-1.442.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.561
r_dihedral_angle_4_deg16.302
r_dihedral_angle_3_deg11.484
r_dihedral_angle_1_deg5.751
r_angle_refined_deg1.671
r_mcangle_it1.66
r_angle_other_deg1.067
r_mcbond_it1.026
r_mcbond_other1.026
r_chiral_restr0.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.561
r_dihedral_angle_4_deg16.302
r_dihedral_angle_3_deg11.484
r_dihedral_angle_1_deg5.751
r_angle_refined_deg1.671
r_mcangle_it1.66
r_angle_other_deg1.067
r_mcbond_it1.026
r_mcbond_other1.026
r_chiral_restr0.18
r_bond_refined_d0.01
r_gen_planes_refined0.007
r_bond_other_d0.006
r_gen_planes_other0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9458
Nucleic Acid Atoms
Solvent Atoms1262
Heterogen Atoms201

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
HKL-3000data scaling