6NDI

Crystal Structure of the Sugar Binding Domain of LacI Family Protein from Klebsiella pneumoniae


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7292Protein: 3.0 mg/ml, 0.01M Tris-HCl pH 8.3; Screen: Classics II (C1), 3.5M Sodium formate pH 7.0; Cryo: 4.0M Sodium formate.
Crystal Properties
Matthews coefficientSolvent content
2.551

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 180.737α = 90
b = 110.478β = 97.94
c = 37.777γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDC(111)2018-11-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.97856APS21-ID-G

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)Rrim I (All)Rpim I (All)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
12.63099.90.1140.1140.1240.04919.36.322623-355.2
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.62.641000.8040.8040.8750.3420.8672.36.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONSADTHROUGHOUT2.629.8321591100799.720.184470.182220.23513RANDOM58.782
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]
1.22-0.7-2.251.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg19.468
r_dihedral_angle_4_deg9.878
r_dihedral_angle_3_deg8.988
r_long_range_B_refined8.755
r_long_range_B_other8.718
r_mcangle_it4.756
r_mcangle_other4.755
r_scangle_other4.648
r_mcbond_it2.764
r_mcbond_other2.764
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg19.468
r_dihedral_angle_4_deg9.878
r_dihedral_angle_3_deg8.988
r_long_range_B_refined8.755
r_long_range_B_other8.718
r_mcangle_it4.756
r_mcangle_other4.755
r_scangle_other4.648
r_mcbond_it2.764
r_mcbond_other2.764
r_scbond_it2.706
r_scbond_other2.706
r_dihedral_angle_1_deg1.888
r_angle_refined_deg1.395
r_angle_other_deg0.368
r_chiral_restr0.066
r_gen_planes_refined0.053
r_gen_planes_other0.048
r_bond_refined_d0.005
r_bond_other_d0.001
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 Atoms4216
Nucleic Acid Atoms
Solvent Atoms157
Heterogen Atoms

Software

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