2Y7P

DntR Inducer Binding Domain in Complex with Salicylate. Trigonal crystal form


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherINITIAL S-SAD MODEL

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
10.2 M NA/K TARTRATE, 0.1 M TRIS PH 8.0-8.5; PEG 8000 28-30%
Crystal Properties
Matthews coefficientSolvent content
3.6366.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 95.698α = 90
b = 95.698β = 90
c = 67.404γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDMIRRORSMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-11.82, 0.976ESRFID23-1

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
11.8552.398.90.0911.24.82971622.2
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)
11.851.999.80.552.94.8

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 DIFFRACTIONS-SAD/MOLECULAR REPLACEMENTTHROUGHOUTINITIAL S-SAD MODEL1.8582.7628765152698.50.181820.180010.21599RANDOM24.175
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]
-0.72-0.36-0.721.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.042
r_dihedral_angle_4_deg20.137
r_dihedral_angle_3_deg15.337
r_dihedral_angle_1_deg6.752
r_scangle_it4.581
r_scbond_it2.899
r_mcangle_it2.023
r_angle_refined_deg1.884
r_mcbond_it1.187
r_chiral_restr0.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.042
r_dihedral_angle_4_deg20.137
r_dihedral_angle_3_deg15.337
r_dihedral_angle_1_deg6.752
r_scangle_it4.581
r_scbond_it2.899
r_mcangle_it2.023
r_angle_refined_deg1.884
r_mcbond_it1.187
r_chiral_restr0.14
r_bond_refined_d0.022
r_gen_planes_refined0.011
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 Atoms1704
Nucleic Acid Atoms
Solvent Atoms181
Heterogen Atoms43

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
SHELXDphasing
SHELXEphasing
PHASERphasing