2VMD

Structure of the complex of discoidin II from Dictyostelium discoideum with beta-methyl-galactose


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.525 % PEG550 MME, pH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.8456.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.14α = 90
b = 81.14β = 90
c = 259.28γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2006-12-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID29ESRFID29

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
11.936.799.70.068.74.4261942
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)
11.92.0198.60.312.354.06

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 2VM91.936.7424868132699.60.1810.1780.227RANDOM25.9
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]
1.580.791.58-2.37
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.856
r_dihedral_angle_4_deg19.319
r_dihedral_angle_3_deg13.827
r_dihedral_angle_1_deg7.426
r_scangle_it3.483
r_scbond_it2.361
r_angle_refined_deg1.494
r_mcangle_it1.465
r_mcbond_it0.878
r_nbtor_refined0.309
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.856
r_dihedral_angle_4_deg19.319
r_dihedral_angle_3_deg13.827
r_dihedral_angle_1_deg7.426
r_scangle_it3.483
r_scbond_it2.361
r_angle_refined_deg1.494
r_mcangle_it1.465
r_mcbond_it0.878
r_nbtor_refined0.309
r_symmetry_vdw_refined0.229
r_nbd_refined0.207
r_symmetry_hbond_refined0.15
r_xyhbond_nbd_refined0.137
r_chiral_restr0.108
r_bond_refined_d0.014
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 Atoms228
Heterogen Atoms37

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
AMoREphasing