4CV3 | pdb_00004cv3

Crystal structure of E. coli FabI in complex with NADH and PT166


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.60.1 M NA-CITRATE PH 5.6, 0.2 M NH4AC, 10% PEG 8000
Crystal Properties
Matthews coefficientSolvent content
2.6954.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.678α = 90
b = 79.678β = 90
c = 330.15γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2013-05-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-1ESRFID23-1

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
11.9547.799.50.112.66.6462436
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)
11.952.0698.60.652.77.1

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1QSG1.956943820233899.130.177990.17620.180.212060.22RANDOM37.903
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]
0.080.040.08-0.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.382
r_dihedral_angle_4_deg15.616
r_dihedral_angle_3_deg14.146
r_dihedral_angle_1_deg7.275
r_scangle_it6.145
r_scbond_it4.161
r_mcangle_it2.586
r_angle_refined_deg1.774
r_mcbond_it1.732
r_chiral_restr0.109
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.382
r_dihedral_angle_4_deg15.616
r_dihedral_angle_3_deg14.146
r_dihedral_angle_1_deg7.275
r_scangle_it6.145
r_scbond_it4.161
r_mcangle_it2.586
r_angle_refined_deg1.774
r_mcbond_it1.732
r_chiral_restr0.109
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 Atoms3536
Nucleic Acid Atoms
Solvent Atoms246
Heterogen Atoms132

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing