2VMC

Structure of the complex of discoidin II from Dictyostelium discoideum with N-acetyl-galactosamine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2VM9PDB ENTRY 2VM9

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.525% PEG5550MME, 100 MM HEPES PH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.9658.53

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.52α = 90
b = 82.52β = 90
c = 261.6γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2006-11-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-1ESRFID14-1

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
11.948.21000.16.56275542
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)
11.921000.342.16.1

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2VM91.943.62616213921000.1590.1570.198RANDOM16.44
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]
0.370.190.37-0.56
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.198
r_dihedral_angle_4_deg17.647
r_dihedral_angle_3_deg12.278
r_dihedral_angle_1_deg7.196
r_scangle_it2.945
r_scbond_it2.018
r_angle_refined_deg1.412
r_mcangle_it1.316
r_mcbond_it0.79
r_nbtor_refined0.297
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.198
r_dihedral_angle_4_deg17.647
r_dihedral_angle_3_deg12.278
r_dihedral_angle_1_deg7.196
r_scangle_it2.945
r_scbond_it2.018
r_angle_refined_deg1.412
r_mcangle_it1.316
r_mcbond_it0.79
r_nbtor_refined0.297
r_nbd_refined0.191
r_symmetry_vdw_refined0.184
r_xyhbond_nbd_refined0.142
r_symmetry_hbond_refined0.121
r_chiral_restr0.109
r_bond_refined_d0.016
r_gen_planes_refined0.006
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_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 Atoms1986
Nucleic Acid Atoms
Solvent Atoms358
Heterogen Atoms64

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
AMoREphasing