5YGM

Monomeric structure of concanavalin A at pH 7.5 from Carnivalia ensiformis


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5298PEK6K, MPD in HEPES, pH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.2645.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.303α = 90
b = 86.59β = 90
c = 89.511γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2702017-06-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPAL/PLS BEAMLINE 7A (6B, 6C1)1.000PAL/PLS7A (6B, 6C1)

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.644.7698.828.26.932123
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.61.6892.8

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 REPLACEMENTTHROUGHOUT1C571.644.7630527158798.650.16730.165840.19648RANDOM19.108
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]
0.710.41-1.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.518
r_dihedral_angle_4_deg15.443
r_dihedral_angle_3_deg13.185
r_dihedral_angle_1_deg7.398
r_long_range_B_refined5.63
r_scbond_it3.325
r_mcangle_it2.665
r_angle_refined_deg2.326
r_mcbond_it1.83
r_chiral_restr0.204
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.518
r_dihedral_angle_4_deg15.443
r_dihedral_angle_3_deg13.185
r_dihedral_angle_1_deg7.398
r_long_range_B_refined5.63
r_scbond_it3.325
r_mcangle_it2.665
r_angle_refined_deg2.326
r_mcbond_it1.83
r_chiral_restr0.204
r_bond_refined_d0.026
r_gen_planes_refined0.014
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1809
Nucleic Acid Atoms
Solvent Atoms238
Heterogen Atoms2

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata processing
SCALAdata scaling
PHASERphasing
Cootmodel building