4UNV

Covalent dimer of lambda variable domains


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3MCGPDB ENTRY 3MCG

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
14.60.1M CH3COONA PH4.6, 2M (NH4)2SO4
Crystal Properties
Matthews coefficientSolvent content
1.831

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 37.417α = 90
b = 60.212β = 90
c = 79.417γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU CCDMIRRORS2013-05-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU

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
11.630980.06397113503
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)
11.61.64860.44.23.6

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 3MCG1.630.111135056897.730.196120.19290.25793RANDOM22.659
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.178
r_dihedral_angle_4_deg18.968
r_dihedral_angle_3_deg14.803
r_dihedral_angle_1_deg6.589
r_scbond_it2.858
r_mcangle_it2.795
r_mcbond_it2
r_mcbond_other1.986
r_angle_refined_deg1.962
r_angle_other_deg0.924
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.178
r_dihedral_angle_4_deg18.968
r_dihedral_angle_3_deg14.803
r_dihedral_angle_1_deg6.589
r_scbond_it2.858
r_mcangle_it2.795
r_mcbond_it2
r_mcbond_other1.986
r_angle_refined_deg1.962
r_angle_other_deg0.924
r_chiral_restr0.119
r_bond_refined_d0.018
r_gen_planes_refined0.01
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_it
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 Atoms783
Nucleic Acid Atoms
Solvent Atoms113
Heterogen Atoms10

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing