2BOI

1.1A Structure of Chromobacterium Violaceum Lectin CV2L in Complex with alpha-methyl-fucoside


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1GZTPDB ENTRY 1GZT

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1PEG 8000 10%, 0.1 M (NH4)2SO4 PH 5
Crystal Properties
Matthews coefficientSolvent content
2.245

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.093α = 90
b = 89.836β = 90
c = 46.479γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDMIRRORS2004-07-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-2ESRFID14-2

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
11.134.381000.075.368.1487549
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)
11.11.131000.32.347.04

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1GZT1.146.478309943891000.1020.1010.117RANDOM
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.699
r_dihedral_angle_3_deg12.545
r_dihedral_angle_4_deg10.834
r_dihedral_angle_1_deg6.881
r_scangle_it4.001
r_scbond_it2.778
r_mcangle_it2.143
r_angle_refined_deg1.634
r_mcbond_it1.606
r_angle_other_deg0.844
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.699
r_dihedral_angle_3_deg12.545
r_dihedral_angle_4_deg10.834
r_dihedral_angle_1_deg6.881
r_scangle_it4.001
r_scbond_it2.778
r_mcangle_it2.143
r_angle_refined_deg1.634
r_mcbond_it1.606
r_angle_other_deg0.844
r_mcbond_other0.657
r_symmetry_vdw_refined0.331
r_symmetry_vdw_other0.29
r_nbd_refined0.269
r_symmetry_hbond_refined0.214
r_nbd_other0.201
r_xyhbond_nbd_refined0.167
r_nbtor_refined0.162
r_chiral_restr0.112
r_nbtor_other0.086
r_metal_ion_refined0.05
r_bond_refined_d0.014
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
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 Atoms1668
Nucleic Acid Atoms
Solvent Atoms333
Heterogen Atoms28

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
ACORNphasing