3RRO | pdb_00003rro

Crystal structure of 3-ketoacyl-(acyl-carrier-protein) reductase (FabG) from Vibrio cholerae


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, 5% Tacsimate, 2.6M Ammonium sulfate, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.1442.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.939α = 90
b = 63.939β = 90
c = 190.146γ = 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
122599.80.0610.06118.94.62960529605-3
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)
122.031000.4040.4042.94.51455

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3OP42252700427004143095.940.140910.140910.138850.140.179220.18RANDOM34.23
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]
-6.23-6.2312.46
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.783
r_dihedral_angle_4_deg18.507
r_dihedral_angle_3_deg13.01
r_dihedral_angle_1_deg5.658
r_scangle_it2.931
r_angle_other_deg2.423
r_scbond_it1.843
r_angle_refined_deg1.259
r_mcangle_it0.995
r_mcbond_it0.602
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.783
r_dihedral_angle_4_deg18.507
r_dihedral_angle_3_deg13.01
r_dihedral_angle_1_deg5.658
r_scangle_it2.931
r_angle_other_deg2.423
r_scbond_it1.843
r_angle_refined_deg1.259
r_mcangle_it0.995
r_mcbond_it0.602
r_chiral_restr0.085
r_mcbond_other0.084
r_bond_refined_d0.013
r_bond_other_d0.007
r_gen_planes_refined0.005
r_gen_planes_other0.003
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 Atoms3607
Nucleic Acid Atoms
Solvent Atoms198
Heterogen Atoms115

Software

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