8Q83 | pdb_00008q83

Photorhabdus laumondii lectin PLL5 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 MODE7.529320 mM Tris 150 mM NaCl
Crystal Properties
Matthews coefficientSolvent content
3.1661.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 93.712α = 90
b = 102.94β = 90.028
c = 97.476γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2019-06-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.9184BESSY14.1

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
11.69945.51598.80.1180.1380.0690.9936.23.8200282
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)
11.71.790.7840.9170.4680.4661.6

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-VALUE1.69945.5152001491044298.5030.1830.18230.19520.19970.211319.253
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]
-5.1931.7951.9383.256
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.857
r_dihedral_angle_3_deg12.007
r_dihedral_angle_4_deg10.463
r_dihedral_angle_1_deg8.535
r_lrange_it2.277
r_lrange_other2.207
r_angle_refined_deg1.262
r_angle_other_deg1.228
r_mcangle_it1.223
r_mcangle_other1.223
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.857
r_dihedral_angle_3_deg12.007
r_dihedral_angle_4_deg10.463
r_dihedral_angle_1_deg8.535
r_lrange_it2.277
r_lrange_other2.207
r_angle_refined_deg1.262
r_angle_other_deg1.228
r_mcangle_it1.223
r_mcangle_other1.223
r_scangle_it1.151
r_scangle_other1.151
r_mcbond_it0.795
r_mcbond_other0.795
r_scbond_it0.761
r_scbond_other0.761
r_nbd_other0.213
r_symmetry_nbd_other0.181
r_nbd_refined0.17
r_symmetry_nbd_refined0.166
r_nbtor_refined0.163
r_symmetry_xyhbond_nbd_other0.161
r_xyhbond_nbd_refined0.12
r_symmetry_xyhbond_nbd_refined0.105
r_symmetry_nbtor_other0.074
r_chiral_restr0.051
r_gen_planes_refined0.005
r_bond_refined_d0.004
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10562
Nucleic Acid Atoms
Solvent Atoms650
Heterogen Atoms192

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing