4RKR

Crystal structure of LacI family transcriptional regulator from Arthrobacter sp. FB24, target EFI-560007, complex with lactose


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4RKQ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.5Protein: 10 mM bis-tris, 500 mM NaCl, 10% glycerol, 5 mM DTT reservoir: 0.1 M magnesium chloride, 0.1 M MES:HAOH, pH 6.5, 30% (w/v) PEG 400; cryoprotection: reservoir plus 20 mM lactose; vapor diffusion, sitting drop, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
2.1643.51

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 36.936α = 90
b = 124.912β = 96.51
c = 117.043γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315MIRRORS2014-07-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29ANSLSX29A

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
12.25099.10.1410.1417.5352910-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.2398.61.43

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 REPLACEMENTTHROUGHOUT4RKQ2.25051293158898.90.173870.171420.25183RANDOM45.889
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]
1.8-2.30.29-1.52
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.043
r_scbond_it20.971
r_scbond_other20.971
r_scangle_other20.179
r_long_range_B_refined18.724
r_long_range_B_other18.724
r_dihedral_angle_4_deg17.766
r_dihedral_angle_3_deg13.34
r_mcbond_other12.589
r_mcbond_it12.579
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.043
r_scbond_it20.971
r_scbond_other20.971
r_scangle_other20.179
r_long_range_B_refined18.724
r_long_range_B_other18.724
r_dihedral_angle_4_deg17.766
r_dihedral_angle_3_deg13.34
r_mcbond_other12.589
r_mcbond_it12.579
r_mcangle_other12.343
r_mcangle_it12.341
r_dihedral_angle_1_deg5.852
r_angle_refined_deg1.2
r_angle_other_deg0.71
r_chiral_restr0.062
r_bond_refined_d0.007
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7956
Nucleic Acid Atoms
Solvent Atoms446
Heterogen Atoms92

Software

Software
Software NamePurpose
CBASSdata collection
PHASERphasing
ARP/wARPmodel building
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling