8Q7U | pdb_00008q7u

Photorhabdus laumondii lectin PLL in complex with alpha-methyl-fucoside


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5C9L 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE7.527720 mM Tris/HCl 150 mM NaCl
Crystal Properties
Matthews coefficientSolvent content
3.0659.76

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.217α = 90
b = 89.184β = 90
c = 158.773γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2022-10-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)0.9763PETRA III, EMBL c/o DESYP14 (MX2)

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.645.5551000.0840.0240.99918.613.566905
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.61.691001.0030.2880.8282.812.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)Mean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE1.645.55566903337199.9810.1630.16250.17640.17960.191918.573
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]
1.048-0.381-0.667
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg17.746
r_dihedral_angle_3_deg11.52
r_dihedral_angle_2_deg8.302
r_dihedral_angle_1_deg8.068
r_lrange_it5.151
r_lrange_other4.995
r_scangle_it4.015
r_scangle_other4.014
r_mcangle_other2.774
r_mcangle_it2.77
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg17.746
r_dihedral_angle_3_deg11.52
r_dihedral_angle_2_deg8.302
r_dihedral_angle_1_deg8.068
r_lrange_it5.151
r_lrange_other4.995
r_scangle_it4.015
r_scangle_other4.014
r_mcangle_other2.774
r_mcangle_it2.77
r_scbond_it2.747
r_scbond_other2.746
r_mcbond_it2.021
r_mcbond_other2.021
r_angle_refined_deg1.679
r_angle_other_deg0.618
r_symmetry_nbd_other0.191
r_nbd_refined0.184
r_nbtor_refined0.177
r_nbd_other0.159
r_symmetry_nbd_refined0.157
r_symmetry_xyhbond_nbd_refined0.157
r_xyhbond_nbd_refined0.131
r_chiral_restr0.095
r_symmetry_nbtor_other0.087
r_bond_refined_d0.011
r_gen_planes_refined0.011
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2726
Nucleic Acid Atoms
Solvent Atoms316
Heterogen Atoms31

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing