2ZX3 | pdb_00002zx3

Rhamnose-binding lectin CSL3


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2ZX0PDB ENTRY 2ZX0

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.929115% PEG8000, 50mM potassium phosphate, 80mM melibiose, pH4.9, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.3647.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.661α = 90
b = 74.733β = 90
c = 94.549γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAC Science DIP-2030mirrors2008-09-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEMACSCIENCE1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
12.1896.40.07622.8233582251711
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.12.1793.40.2138.1

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2ZX02.182134311501000.183820.180840.180.24020.24RANDOM17.655
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]
0.49-0.630.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg26.979
r_dihedral_angle_4_deg9.016
r_dihedral_angle_3_deg8.567
r_dihedral_angle_1_deg2.709
r_scangle_it2.429
r_scbond_it1.51
r_angle_refined_deg1.509
r_mcangle_it0.918
r_mcbond_it0.561
r_nbtor_refined0.304
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg26.979
r_dihedral_angle_4_deg9.016
r_dihedral_angle_3_deg8.567
r_dihedral_angle_1_deg2.709
r_scangle_it2.429
r_scbond_it1.51
r_angle_refined_deg1.509
r_mcangle_it0.918
r_mcbond_it0.561
r_nbtor_refined0.304
r_nbd_refined0.196
r_symmetry_hbond_refined0.179
r_xyhbond_nbd_refined0.155
r_symmetry_vdw_refined0.152
r_chiral_restr0.088
r_bond_refined_d0.009
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3027
Nucleic Acid Atoms
Solvent Atoms340
Heterogen Atoms102

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data collection
DENZOdata reduction
HKL-2000data scaling
MOLREPphasing