2BV4

1.0A Structure of Chromobacterium Violaceum Lectin in Complex with alpha-methyl-mannoside


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1PEG 8000 10%, 0.1M NACL
Crystal Properties
Matthews coefficientSolvent content
2.244

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.685α = 90
b = 89.504β = 90
c = 46.484γ = 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
1123.2499.60.066.487.02114226
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)
111.0394.40.441.673.04

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 1GZT146.47108432572499.50.1070.1070.123RANDOM7.02
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]
0.59-0.43-0.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.912
r_dihedral_angle_4_deg16.651
r_dihedral_angle_3_deg12.514
r_dihedral_angle_1_deg6.991
r_scangle_it3.896
r_scbond_it2.773
r_mcangle_it2.107
r_angle_other_deg2.094
r_angle_refined_deg1.745
r_mcbond_it1.557
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.912
r_dihedral_angle_4_deg16.651
r_dihedral_angle_3_deg12.514
r_dihedral_angle_1_deg6.991
r_scangle_it3.896
r_scbond_it2.773
r_mcangle_it2.107
r_angle_other_deg2.094
r_angle_refined_deg1.745
r_mcbond_it1.557
r_mcbond_other0.621
r_chiral_restr0.351
r_symmetry_vdw_other0.262
r_nbd_refined0.261
r_symmetry_vdw_refined0.254
r_xyhbond_nbd_refined0.24
r_symmetry_hbond_refined0.236
r_nbd_other0.207
r_nbtor_refined0.169
r_nbtor_other0.102
r_metal_ion_refined0.053
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 Atoms380
Heterogen Atoms30

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
ACORNphasing