5YQW

Structure and function of a novel periplasmic chitooligosaccharide-binding protein from marine Vibrio bacteria


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1ZU0 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5293.150.09M Halogens (NaF, NaBr, NaI), 0.1M Buffer 2 (HEPES/MOPS) pH 7.5, 37.5% MPD_P1K_P3350 mix
Crystal Properties
Matthews coefficientSolvent content
2.3247

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.73α = 90
b = 54.73β = 90
c = 306.442γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray95PIXELDECTRIS PILATUS 6M-FFixed monochromator2017-05-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.92819DiamondI04-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
11.3646.899.80.1320.1390.0440.9957.69.5115984
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.361.497.71.6591.8070.9480.0671.26.8

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1ZU01.3646.84107022547396.670.196660.195140.22622RANDOM17.552
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]
0.270.130.27-0.86
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.823
r_dihedral_angle_4_deg16.967
r_dihedral_angle_3_deg13.533
r_dihedral_angle_1_deg6.673
r_long_range_B_refined5.376
r_scbond_it2.935
r_mcangle_it2.226
r_angle_refined_deg2.209
r_mcbond_it1.599
r_chiral_restr0.185
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.823
r_dihedral_angle_4_deg16.967
r_dihedral_angle_3_deg13.533
r_dihedral_angle_1_deg6.673
r_long_range_B_refined5.376
r_scbond_it2.935
r_mcangle_it2.226
r_angle_refined_deg2.209
r_mcbond_it1.599
r_chiral_restr0.185
r_bond_refined_d0.03
r_gen_planes_refined0.016
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_it
r_scangle_other
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 Atoms4260
Nucleic Acid Atoms
Solvent Atoms461
Heterogen Atoms52

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing