5C9L | pdb_00005c9l

Crystal structure of native PLL lectin from Photorhabdus luminescens at 1.65 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.52900.1 M Tris-HCl, 10% PEG 4000, 0.2 M CaCl2, pH 8.5
Crystal Properties
Matthews coefficientSolvent content
2.9658.48

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.12α = 90
b = 87.677β = 90
c = 157.691γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2013-08-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)1.005PETRA 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
11.6576.7599.70.04836.213.559360
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)
11.651.7499.10.15414.413.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONSADTHROUGHOUT1.6539.1556352300199.60.141580.140630.15310.158940.1694RANDOM14.117
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]
0.280.07-0.35
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.512
r_dihedral_angle_4_deg15.513
r_dihedral_angle_3_deg11.615
r_dihedral_angle_1_deg7.783
r_long_range_B_refined5.874
r_long_range_B_other5.563
r_scangle_other3.882
r_scbond_it2.821
r_scbond_other2.812
r_mcangle_it2.762
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.512
r_dihedral_angle_4_deg15.513
r_dihedral_angle_3_deg11.615
r_dihedral_angle_1_deg7.783
r_long_range_B_refined5.874
r_long_range_B_other5.563
r_scangle_other3.882
r_scbond_it2.821
r_scbond_other2.812
r_mcangle_it2.762
r_mcangle_other2.762
r_angle_refined_deg2.397
r_mcbond_it1.952
r_mcbond_other1.95
r_angle_other_deg1.244
r_chiral_restr0.169
r_bond_refined_d0.068
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 Atoms2743
Nucleic Acid Atoms
Solvent Atoms373
Heterogen Atoms63

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
SHELXDEphasing