6RGJ

Photorhabdus asymbiotica lectin PHL in complex with D-glucose


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52933.9 M NaCl, 100 mM Hepes, pH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.8456.69

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.638α = 90
b = 80.638β = 90
c = 113.437γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2016-08-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.30.8950BESSY14.3

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.844.0399.70.1440.99818.512.34011210.799
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.998.20.7950.8954.512.1

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 REPLACEMENTTHROUGHOUT5MXE1.844.0338051202199.680.171120.169820.1965RANDOM15.492
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]
0.290.140.29-0.93
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.529
r_dihedral_angle_4_deg14.4
r_dihedral_angle_3_deg11.384
r_dihedral_angle_1_deg8.508
r_long_range_B_refined4.079
r_long_range_B_other3.684
r_scangle_other1.798
r_mcangle_it1.528
r_mcangle_other1.527
r_angle_refined_deg1.4
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.529
r_dihedral_angle_4_deg14.4
r_dihedral_angle_3_deg11.384
r_dihedral_angle_1_deg8.508
r_long_range_B_refined4.079
r_long_range_B_other3.684
r_scangle_other1.798
r_mcangle_it1.528
r_mcangle_other1.527
r_angle_refined_deg1.4
r_angle_other_deg1.361
r_scbond_it1.145
r_scbond_other1.145
r_mcbond_it0.941
r_mcbond_other0.941
r_chiral_restr0.061
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
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 Atoms2654
Nucleic Acid Atoms
Solvent Atoms355
Heterogen Atoms71

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing