5IP4 | pdb_00005ip4

X-RAY STRUCTURE OF THE C-TERMINAL DOMAIN OF HUMAN DOUBLECORTIN


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2X1OENSEMBLE OF 2X1O, 2X1P, 2X6M, 3DWT, 3EAK, 3G9A, AND 3P0G
experimental modelPDB 2X1PENSEMBLE OF 2X1O, 2X1P, 2X6M, 3DWT, 3EAK, 3G9A, AND 3P0G
experimental modelPDB 2X6MENSEMBLE OF 2X1O, 2X1P, 2X6M, 3DWT, 3EAK, 3G9A, AND 3P0G
experimental modelPDB 3DWTENSEMBLE OF 2X1O, 2X1P, 2X6M, 3DWT, 3EAK, 3G9A, AND 3P0G
experimental modelPDB 3EAKENSEMBLE OF 2X1O, 2X1P, 2X6M, 3DWT, 3EAK, 3G9A, AND 3P0G
experimental modelPDB 3G9AENSEMBLE OF 2X1O, 2X1P, 2X6M, 3DWT, 3EAK, 3G9A, AND 3P0G
experimental modelPDB 3P0GENSEMBLE OF 2X1O, 2X1P, 2X6M, 3DWT, 3EAK, 3G9A, AND 3P0G

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION6.529320% PEGMME, 100 mM Bis-Tris pH 6.5
Crystal Properties
Matthews coefficientSolvent content
2.856.08

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.84α = 90
b = 86.191β = 123
c = 73.267γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2011-05-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA1.00SLSX10SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Rrim I (All)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
11.8144.7799.80.0670.07710.333.4242622
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.811.999.71.11.273.28

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTENSEMBLE OF 2X1O, 2X1P, 2X6M, 3DWT, 3EAK, 3G9A, AND 3P0G1.8144.7738934206395.950.19670.193980.190.246350.24RANDOM31.575
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]
0.830.46-0.370.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.236
r_dihedral_angle_4_deg25.687
r_dihedral_angle_3_deg16.083
r_dihedral_angle_1_deg6.528
r_angle_refined_deg2.121
r_chiral_restr0.152
r_bond_refined_d0.019
r_gen_planes_refined0.011
r_bond_other_d
r_angle_other_deg
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2986
Nucleic Acid Atoms
Solvent Atoms387
Heterogen Atoms

Software

Software
Software NamePurpose
XDSdata reduction
SADABSdata scaling
REFMACrefinement
PHASERphasing