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 (32 uM) and mannose-squaramide (128 uM) + 1 uL crystallization condition (Helix screen, condition B6: 0.1 M sodium chloride, 0.005 M strontium chloride hexahydrate, 0.05 M MES (pH 6.5), 17% w/v PEG 4000). Reservoir contained 70 uL of crystallization condition.
Crystal Properties
Matthews coefficientSolvent content
2.3146.75

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.42α = 90
b = 86.13β = 90
c = 89.5γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-3002020-07-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.9786APS21-ID-G

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.862.0699.80.1482.54659.1121234
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.91000.638.95

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 REPLACEMENTTHROUGHOUT1JBC1.862.0621234111499.80.1860.1840.23RANDOM17.64
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]
1.69-0.34-1.35
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.37
r_dihedral_angle_4_deg20.881
r_dihedral_angle_3_deg11.852
r_dihedral_angle_1_deg8.359
r_long_range_B_refined5.943
r_long_range_B_other5.577
r_scangle_other3.02
r_mcangle_it2.261
r_mcangle_other2.26
r_scbond_it1.971
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.37
r_dihedral_angle_4_deg20.881
r_dihedral_angle_3_deg11.852
r_dihedral_angle_1_deg8.359
r_long_range_B_refined5.943
r_long_range_B_other5.577
r_scangle_other3.02
r_mcangle_it2.261
r_mcangle_other2.26
r_scbond_it1.971
r_scbond_other1.965
r_angle_refined_deg1.56
r_mcbond_it1.463
r_mcbond_other1.458
r_angle_other_deg1.369
r_chiral_restr0.066
r_bond_refined_d0.01
r_gen_planes_refined0.009
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 Atoms1761
Nucleic Acid Atoms
Solvent Atoms259
Heterogen Atoms2

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing