5F7R

ROK repressor Lmo0178 from Listeria monocytogenes bound to inducer


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP3009.0 mg/mL protein in 0.5 M sodium chloride, 0.01 M Tris-HCl, pH 8.3 against Classics II D6 (Qiagen, 0.1 M Bis-Tris, pH 5.5, 25% w/v PEG3350)
Crystal Properties
Matthew coefficientSolvent content
1.7730.34

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.2α = 90
b = 95.064β = 90
c = 117.144γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2015-04-27MSINGLE 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
11.83099.90.05124.15.655352
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)
11.81.851000.5672.75.6

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 REPLACEMENTTHROUGHOUTin-house structure1.853052630266499.790.16820.166590.20029RANDOM32.369
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]
0.3-0.06-0.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.52
r_dihedral_angle_4_deg19.465
r_dihedral_angle_3_deg13.913
r_dihedral_angle_1_deg6.486
r_long_range_B_other5.263
r_long_range_B_refined5.263
r_scangle_other2.378
r_mcangle_it1.754
r_mcangle_other1.754
r_scbond_it1.454
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.52
r_dihedral_angle_4_deg19.465
r_dihedral_angle_3_deg13.913
r_dihedral_angle_1_deg6.486
r_long_range_B_other5.263
r_long_range_B_refined5.263
r_scangle_other2.378
r_mcangle_it1.754
r_mcangle_other1.754
r_scbond_it1.454
r_scbond_other1.442
r_angle_refined_deg1.253
r_mcbond_it1.07
r_mcbond_other1.069
r_angle_other_deg0.76
r_chiral_restr0.081
r_bond_refined_d0.009
r_gen_planes_refined0.008
r_gen_planes_other0.002
r_bond_other_d0.001
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_scangle_it
r_metal_ion_refined
r_metal_ion_other
r_sphericity_bonded
r_rigid_bond_restr
r_sphericity_free
r_symmetry_vdw_refined
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4731
Nucleic Acid Atoms
Solvent Atoms264
Heterogen Atoms61

Software

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