5MXE

Photorhabdus asymbiotica lectin (PHL) in free form


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5C9O 

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
2.6954.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.235α = 90
b = 81.235β = 90
c = 113.441γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944+2014-10-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.5418

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
11.944.1698.80.0710.99714.73.634331
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)
11.9293.40.2370.9342.5

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 REPLACEMENTTHROUGHOUT5C9O1.944.1632591170298.770.16760.166380.19101RANDOM12.541
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]
0.040.020.04-0.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.247
r_dihedral_angle_3_deg11.121
r_dihedral_angle_4_deg8.28
r_dihedral_angle_1_deg7.698
r_long_range_B_refined3.908
r_long_range_B_other3.242
r_angle_refined_deg1.308
r_scangle_other1.17
r_mcangle_it1.126
r_mcangle_other1.125
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.247
r_dihedral_angle_3_deg11.121
r_dihedral_angle_4_deg8.28
r_dihedral_angle_1_deg7.698
r_long_range_B_refined3.908
r_long_range_B_other3.242
r_angle_refined_deg1.308
r_scangle_other1.17
r_mcangle_it1.126
r_mcangle_other1.125
r_angle_other_deg0.953
r_scbond_it0.709
r_scbond_other0.709
r_mcbond_other0.65
r_mcbond_it0.649
r_chiral_restr0.093
r_bond_refined_d0.009
r_gen_planes_refined0.004
r_bond_other_d0.002
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 Atoms2664
Nucleic Acid Atoms
Solvent Atoms363
Heterogen Atoms12

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing