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) + 1 uL crystallization condition (Helix screen, condition H3: 0.1 M potassium chloride, 0.005 M barium chloride dihydrate, 0.05 M bis-Tris (pH 7), 12% w/v PEG 8000). Reservoir contained 70 uL of crystallization condition.
Crystal Properties
Matthews coefficientSolvent content
2.2745.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.19α = 90
b = 85.18β = 90
c = 89.25γ = 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
1261.6292.20.1123.1997.1214120
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)
122.1182.40.446.26

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 REPLACEMENTTHROUGHOUT1JBC261.621412077092.20.2060.2030.262RANDOM22.22
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]
1.34-0.09-1.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.196
r_dihedral_angle_4_deg19.982
r_dihedral_angle_3_deg11.817
r_dihedral_angle_1_deg8.776
r_long_range_B_refined4.534
r_long_range_B_other4.458
r_scangle_other2.814
r_mcangle_it2.396
r_mcangle_other2.396
r_scbond_it1.84
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.196
r_dihedral_angle_4_deg19.982
r_dihedral_angle_3_deg11.817
r_dihedral_angle_1_deg8.776
r_long_range_B_refined4.534
r_long_range_B_other4.458
r_scangle_other2.814
r_mcangle_it2.396
r_mcangle_other2.396
r_scbond_it1.84
r_scbond_other1.831
r_mcbond_it1.553
r_mcbond_other1.542
r_angle_refined_deg1.516
r_angle_other_deg1.292
r_chiral_restr0.064
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 Atoms1753
Nucleic Acid Atoms
Solvent Atoms161
Heterogen Atoms2

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing