X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1JBC 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7295Sitting drop comprising 1 uL of Concanavalin A (80 uM) and Man-CGCG (160 uM) + 1 uL crystallization condition (Helix screen, condition D9: 0.05 M bis-Tris (pH 7), 2 M ammonium sulfate, 5% v/v PEG 400). Reservoir contained 70 uL of crystallization condition
Crystal Properties
Matthews coefficientSolvent content
2.7855.71

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.419α = 90
b = 69.92β = 90
c = 125.869γ = 90
Symmetry
Space GroupP 21 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 9M2019-10-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-D1.1271APS21-ID-D

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)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
1369.9298.180.1970.2092.52729.3511395
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
133.1699.970.660.69310.05

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 REPLACEMENTTHROUGHOUT1JBC369.921139565298.180.236050.233170.28446RANDOM57.774
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]
-3.963.550.41
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.677
r_dihedral_angle_3_deg14.973
r_scangle_other9.973
r_dihedral_angle_1_deg8.112
r_dihedral_angle_4_deg7.942
r_mcangle_other7.887
r_mcangle_it7.885
r_scbond_it6.63
r_scbond_other6.628
r_mcbond_it5.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.677
r_dihedral_angle_3_deg14.973
r_scangle_other9.973
r_dihedral_angle_1_deg8.112
r_dihedral_angle_4_deg7.942
r_mcangle_other7.887
r_mcangle_it7.885
r_scbond_it6.63
r_scbond_other6.628
r_mcbond_it5.15
r_mcbond_other5.134
r_angle_refined_deg1.593
r_angle_other_deg1.262
r_chiral_restr0.169
r_bond_refined_d0.008
r_gen_planes_refined0.006
r_bond_other_d0.001
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 Atoms3284
Nucleic Acid Atoms164
Solvent Atoms22
Heterogen Atoms68

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing