3RSH

Structure of 3-ketoacyl-(acyl-carrier-protein)reductase (FabG) from Vibrio cholerae O1 complexed with NADP+ (space group P62)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3OP4 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP92890.1M Tris pH9.0, 2.6M Ammonium Sulfate, 5% Tacsimate, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.1241.92

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.776α = 90
b = 63.776β = 90
c = 190.18γ = 120
Symmetry
Space GroupP 62

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rMirrors2011-03-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.9792APS19-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.9550990.080.06326.44.43159631596-326.3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.951.9899.60.5930.5933.23.81606

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3OP41.9550.012993529935161199.120.133770.133770.132550.15568RANDOM31.466
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]
11.111.1-22.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.39
r_dihedral_angle_4_deg15.212
r_dihedral_angle_3_deg13.567
r_dihedral_angle_1_deg5.54
r_scangle_it2.429
r_scbond_it1.476
r_angle_refined_deg1.261
r_mcangle_it0.89
r_angle_other_deg0.857
r_mcbond_it0.51
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.39
r_dihedral_angle_4_deg15.212
r_dihedral_angle_3_deg13.567
r_dihedral_angle_1_deg5.54
r_scangle_it2.429
r_scbond_it1.476
r_angle_refined_deg1.261
r_mcangle_it0.89
r_angle_other_deg0.857
r_mcbond_it0.51
r_mcbond_other0.137
r_chiral_restr0.069
r_bond_refined_d0.01
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3570
Nucleic Acid Atoms
Solvent Atoms149
Heterogen Atoms167

Software

Software
Software NamePurpose
HKL-3000data collection
HKL-3000phasing
MOLREPphasing
REFMACrefinement
Cootmodel building
HKL-3000data reduction
HKL-3000data scaling