5MXF

Photorhabdus asymbiotica lectin (PHL) in complex with alpha-methyl fucoside


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52903.7-4.3 M NaCl, 100 mM Hepes pH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.6854.16

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.249α = 90
b = 81.249β = 90
c = 113.231γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2013-12-06MSINGLE 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)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
11.944.111000.0760.99922.410.734705
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)
11.921000.4570.9455.311

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 REPLACEMENTTHROUGHOUT5MXE1.944.1132917174699.990.168710.167240.19573RANDOM23.486
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]
0.290.140.29-0.93
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.853
r_dihedral_angle_3_deg10.896
r_dihedral_angle_1_deg7.742
r_dihedral_angle_4_deg6.726
r_long_range_B_refined3.843
r_long_range_B_other3.423
r_scangle_other2.022
r_mcangle_it1.7
r_mcangle_other1.7
r_angle_refined_deg1.306
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.853
r_dihedral_angle_3_deg10.896
r_dihedral_angle_1_deg7.742
r_dihedral_angle_4_deg6.726
r_long_range_B_refined3.843
r_long_range_B_other3.423
r_scangle_other2.022
r_mcangle_it1.7
r_mcangle_other1.7
r_angle_refined_deg1.306
r_scbond_it1.302
r_scbond_other1.301
r_mcbond_it1.124
r_mcbond_other1.123
r_angle_other_deg0.936
r_chiral_restr0.089
r_bond_refined_d0.009
r_bond_other_d0.006
r_gen_planes_refined0.005
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 Atoms2672
Nucleic Acid Atoms
Solvent Atoms303
Heterogen Atoms36

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing