5C9O | pdb_00005c9o

Crystal structure of recombinant PLL lectin from Photorhabdus luminescens at 1.5 A resolution


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.5290.150.1 M Tris-HCl, 2.5 % ethanol, pH 8.5
Crystal Properties
Matthews coefficientSolvent content
2.9157.78

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.787α = 90
b = 87.825β = 90
c = 158.336γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2013-10-31MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)0.967PETRA III, EMBL c/o DESYP13 (MX1)

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.579.171000.06228.213.480153
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.51.581000.3616.913.6

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT5C9L1.539.1776120402399.920.132080.131070.130.15170.15RANDOM13.465
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]
0.370.12-0.49
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.875
r_dihedral_angle_4_deg15.268
r_dihedral_angle_3_deg11.987
r_dihedral_angle_1_deg8.464
r_long_range_B_refined5.927
r_long_range_B_other5.588
r_scangle_other4.17
r_scbond_it2.967
r_scbond_other2.952
r_mcangle_other2.789
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.875
r_dihedral_angle_4_deg15.268
r_dihedral_angle_3_deg11.987
r_dihedral_angle_1_deg8.464
r_long_range_B_refined5.927
r_long_range_B_other5.588
r_scangle_other4.17
r_scbond_it2.967
r_scbond_other2.952
r_mcangle_other2.789
r_mcangle_it2.787
r_angle_refined_deg2.534
r_mcbond_it1.837
r_mcbond_other1.792
r_angle_other_deg1.273
r_chiral_restr0.188
r_bond_refined_d0.029
r_gen_planes_refined0.014
r_bond_other_d0.003
r_gen_planes_other0.002
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 Atoms2750
Nucleic Acid Atoms
Solvent Atoms405
Heterogen Atoms102

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing