3DZW

Structure of Narcissus pseudonarcissus lectin complex with Mannobiose at 1.7 A resolution, form II


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1829310 mg/ml in Phosphate buffered saline, containing up to 20mM beta-1,3 mannobiose, pH 8.0, VAPOR DIFFUSION, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.856.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.003α = 90
b = 102.011β = 90
c = 74.366γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray277IMAGE PLATEMAR scanner 300 mm plateMIRROR1996-07-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSRS BEAMLINE PX9.6SRSPX9.6

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.721.03199.20.0770.077330200
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.71.7999.20.3820.3821.83

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 1NPL1.721.03130180152398.960.188230.186840.21279RANDOM18.66
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]
-0.7-0.781.48
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg23.49
r_dihedral_angle_3_deg7.953
r_dihedral_angle_4_deg5.777
r_scangle_it4.649
r_scbond_it3.238
r_dihedral_angle_1_deg2.606
r_angle_other_deg2.461
r_mcangle_it2.199
r_mcbond_it1.91
r_angle_refined_deg1.544
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg23.49
r_dihedral_angle_3_deg7.953
r_dihedral_angle_4_deg5.777
r_scangle_it4.649
r_scbond_it3.238
r_dihedral_angle_1_deg2.606
r_angle_other_deg2.461
r_mcangle_it2.199
r_mcbond_it1.91
r_angle_refined_deg1.544
r_mcbond_other0.54
r_symmetry_hbond_refined0.289
r_nbd_other0.175
r_symmetry_vdw_other0.172
r_nbtor_refined0.158
r_nbd_refined0.157
r_xyhbond_nbd_refined0.145
r_nbtor_other0.096
r_chiral_restr0.095
r_symmetry_vdw_refined0.067
r_bond_refined_d0.018
r_xyhbond_nbd_other0.013
r_bond_other_d0.004
r_gen_planes_refined0.003
r_gen_planes_other0.001
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1716
Nucleic Acid Atoms
Solvent Atoms295
Heterogen Atoms163

Software

Software
Software NamePurpose
SCALAdata scaling
AMoREphasing
REFMACrefinement
PDB_EXTRACTdata extraction