5F7Q

ROK repressor Lmo0178 from Listeria monocytogenes bound to operator


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5F7R 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP3007.5 mg/mL protein in 0.5 M sodium chloride, 0.01 M Tris-HCl, pH 8.3 against Classics II H6 (Qiagen, 0.2 M sodium formate, 20% w/v PEG3350)
Crystal Properties
Matthews coefficientSolvent content
2.6954.23

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.672α = 90
b = 180.257β = 89.97
c = 79.86γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2015-04-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.97872APS21-ID-F

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
12.4301000.06728.75.581757
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)
12.42.441000.715.5

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 REPLACEMENTTHROUGHOUT5F7R2.43077556401099.60.1840.1820.218RANDOM58.79
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]
0.1-0.331.13-1.23
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.465
r_dihedral_angle_4_deg12.913
r_dihedral_angle_3_deg11.384
r_dihedral_angle_1_deg6.165
r_long_range_B_refined6.005
r_long_range_B_other6.005
r_scangle_other4.184
r_mcangle_it3.088
r_mcangle_other3.088
r_scbond_it2.655
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.465
r_dihedral_angle_4_deg12.913
r_dihedral_angle_3_deg11.384
r_dihedral_angle_1_deg6.165
r_long_range_B_refined6.005
r_long_range_B_other6.005
r_scangle_other4.184
r_mcangle_it3.088
r_mcangle_other3.088
r_scbond_it2.655
r_scbond_other2.655
r_mcbond_it1.991
r_mcbond_other1.991
r_angle_refined_deg1.453
r_angle_other_deg0.955
r_chiral_restr0.089
r_gen_planes_refined0.023
r_gen_planes_other0.018
r_bond_refined_d0.01
r_bond_other_d0.002
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 Atoms12220
Nucleic Acid Atoms1394
Solvent Atoms273
Heterogen Atoms163

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing