4D46

Crystal structure of E. coli FabI in complex with NAD and 5-bromo-2-(4-chloro-2-hydroxyphenoxy)benzonitrile


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1QSGPDB ENTRY 1QSG

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
110.50.08 M NH4AC, 0.1 M CAPS PH 10.5, 20% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.5251.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.144α = 90
b = 79.144β = 90
c = 322.316γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2013-04-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.1BESSY14.1

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
1246.961000.1416.219418186
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)
122.111001.252.419.2

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 1QSG268.5439588209999.980.167660.165630.20643RANDOM41.565
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]
2.061.032.06-3.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.794
r_dihedral_angle_4_deg19.438
r_dihedral_angle_3_deg14.2
r_dihedral_angle_1_deg7.234
r_scangle_it5.59
r_scbond_it3.851
r_mcangle_it2.315
r_angle_refined_deg1.752
r_mcbond_it1.616
r_chiral_restr0.107
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.794
r_dihedral_angle_4_deg19.438
r_dihedral_angle_3_deg14.2
r_dihedral_angle_1_deg7.234
r_scangle_it5.59
r_scbond_it3.851
r_mcangle_it2.315
r_angle_refined_deg1.752
r_mcbond_it1.616
r_chiral_restr0.107
r_bond_refined_d0.015
r_gen_planes_refined0.015
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_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 Atoms3604
Nucleic Acid Atoms
Solvent Atoms250
Heterogen Atoms124

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing