9J1F

Dimeric Structure of ConA/M2P-Man


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4P9W 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2980.2M Sodium chloride, 0.1M Phosphate-citrate pH 4.2 10% (w/v) PEG 3000
Crystal Properties
Matthews coefficientSolvent content
2.4549.79

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.216α = 90
b = 79.07β = 117.2
c = 87.917γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2024-06-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL10U20.979SSRFBL10U2

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
12.1778.299.80.1360.1610.0840.9834.43.552760
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)
12.172.2899.40.8621.0580.6020.3692.9

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 REPLACEMENTTHROUGHOUT4P9W2.1778.249425247798.220.210930.20870.2569RANDOM27.965
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]
0.010.02-0.110.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.228
r_dihedral_angle_4_deg20.613
r_dihedral_angle_3_deg14.739
r_dihedral_angle_1_deg8.818
r_long_range_B_refined7.03
r_long_range_B_other7.029
r_mcangle_it4.694
r_mcangle_other4.694
r_scangle_other4.301
r_mcbond_it2.751
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.228
r_dihedral_angle_4_deg20.613
r_dihedral_angle_3_deg14.739
r_dihedral_angle_1_deg8.818
r_long_range_B_refined7.03
r_long_range_B_other7.029
r_mcangle_it4.694
r_mcangle_other4.694
r_scangle_other4.301
r_mcbond_it2.751
r_mcbond_other2.75
r_scbond_it2.583
r_scbond_other2.581
r_angle_refined_deg1.599
r_angle_other_deg1.222
r_chiral_restr0.063
r_bond_refined_d0.008
r_gen_planes_refined0.007
r_gen_planes_other0.002
r_bond_other_d0.001
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 Atoms7236
Nucleic Acid Atoms
Solvent Atoms65
Heterogen Atoms116

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing