2CGY

STRUCTURE OF HELIX POMATIA AGGLUTININ WITH FORSMANN ANTIGEN


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2CE6PDB ENTRY 2CE6

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROPHANGING DROP METHOD WITH PRECIPITATION SOLUTION CONTAINING LITHIUM SULPHATE (2 M) AND AMMONIUM SULPHATE (3.5 M) IN SODIUM CITRATE BUFFER (1.5M, PH 6.5) AND 10MM OF FORSMANN LIGAND.
Crystal Properties
Matthews coefficientSolvent content
2.347.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.019α = 90
b = 62.019β = 90
c = 106.642γ = 120
Symmetry
Space GroupP 63 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDTOROIDAL MIRROR2000-04-08MSINGLE 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
12.83087.90.0717.172945
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)
12.82.993.50.364

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 2CE62.820279213288.10.2650.2620.32RANDOM54.29
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]
-3.92-1.96-3.925.88
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg7.086
r_scangle_it1.348
r_angle_refined_deg1.242
r_scbond_it0.75
r_angle_other_deg0.73
r_mcangle_it0.597
r_symmetry_vdw_refined0.339
r_mcbond_it0.322
r_symmetry_vdw_other0.252
r_nbd_other0.209
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg7.086
r_scangle_it1.348
r_angle_refined_deg1.242
r_scbond_it0.75
r_angle_other_deg0.73
r_mcangle_it0.597
r_symmetry_vdw_refined0.339
r_mcbond_it0.322
r_symmetry_vdw_other0.252
r_nbd_other0.209
r_xyhbond_nbd_refined0.198
r_nbd_refined0.19
r_nbtor_other0.081
r_chiral_restr0.068
r_symmetry_hbond_refined0.013
r_bond_refined_d0.008
r_gen_planes_refined0.003
r_bond_other_d0.002
r_gen_planes_other0.001
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_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 Atoms767
Nucleic Acid Atoms
Solvent Atoms1
Heterogen Atoms43

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing