6RGR

Photorhabdus asymbiotica lectin PHL in complex with L-rhamnose


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52933.8 M NaCl, 100 mM Hepes, pH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.8656.92

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.499α = 90
b = 80.499β = 90
c = 113.413γ = 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 14.30.8943BESSY14.3

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
11.8943.9999.80.1130.99916.112.23461825.4
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)
11.891.9998.61.3170.742212.1

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 REPLACEMENTTHROUGHOUT5MXE1.8943.9932866171299.770.201130.199670.22876RANDOM30.646
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]
0.70.350.7-2.28
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.333
r_dihedral_angle_3_deg11.546
r_dihedral_angle_4_deg9.211
r_dihedral_angle_1_deg8.619
r_long_range_B_refined4.166
r_long_range_B_other4.087
r_scangle_other2.639
r_mcangle_it2.581
r_mcangle_other2.58
r_mcbond_it1.742
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.333
r_dihedral_angle_3_deg11.546
r_dihedral_angle_4_deg9.211
r_dihedral_angle_1_deg8.619
r_long_range_B_refined4.166
r_long_range_B_other4.087
r_scangle_other2.639
r_mcangle_it2.581
r_mcangle_other2.58
r_mcbond_it1.742
r_mcbond_other1.742
r_scbond_it1.739
r_scbond_other1.739
r_angle_refined_deg1.309
r_angle_other_deg1.249
r_chiral_restr0.052
r_bond_refined_d0.006
r_gen_planes_refined0.005
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 Atoms2633
Nucleic Acid Atoms
Solvent Atoms172
Heterogen Atoms37

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing